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A

A - picard.analysis.artifacts.Transition.Base
 
A - picard.illumina.parser.IntensityChannel
 
aa - picard.fingerprint.DiploidHaplotype
 
Aa - picard.fingerprint.DiploidHaplotype
 
AA - picard.arrays.illumina.IlluminaGenotype
 
AA - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
 
AA - picard.fingerprint.DiploidGenotype
 
AA - picard.fingerprint.DiploidHaplotype
 
AA_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
 
AB - picard.arrays.illumina.IlluminaGenotype
 
AB - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
 
AB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
 
AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
The filter string used for sites that fail the allele balance filter.
AbstractAlignmentMerger - Class in picard.sam
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
constructor with a default setting for unmappingReadsStrategy.
AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, AbstractAlignmentMerger.UnmappingReadStrategy) - Constructor for class picard.sam.AbstractAlignmentMerger
Constructor
AbstractAlignmentMerger.UnmappingReadStrategy - Enum in picard.sam
 
AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Use this ctor if lane and tile are not discernible from file name.
AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
 
AbstractInputParser - Class in picard.util
Class for parsing text files where each line consists of fields separated by whitespace.
AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
 
AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
AC - picard.fingerprint.DiploidGenotype
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
 
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to accept SAMRecords one at a time.
acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
acceptRecord(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Adds information about an individual SAMRecord to the statistics.
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
 
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
 
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
 
acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
 
acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
Incorporates the provided variant's data into the metric analysis.
accumulate(VariantContext) - Method in class picard.vcf.GvcfMetricAccumulator
 
accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
 
AccumulateQualityYieldMetrics - Class in picard.util
Combines multiple Picard QualityYieldMetrics files into a single file.
AccumulateQualityYieldMetrics() - Constructor for class picard.util.AccumulateQualityYieldMetrics
 
AccumulateVariantCallingMetrics - Class in picard.vcf
Combines multiple Variant Calling Metrics files into a single file.
AccumulateVariantCallingMetrics() - Constructor for class picard.vcf.AccumulateVariantCallingMetrics
 
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
 
ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
 
accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Returns the VariantProcessor.Accumulators associated with this executor.
accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
ACCURACY - Variable in class picard.sam.DownsampleSam
 
ACGT_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
ACTION - Variable in class picard.util.IntervalListTools
 
ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
 
AdapterMarker - Class in picard.util
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
 
AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
Truncates adapters to DEFAULT_ADAPTER_LENGTH
AdapterPair - Interface in picard.util
 
ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
 
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
 
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
 
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
 
adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
Overrides defaults for minMatchBases and maxErrorRate
adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
Invokes adapterTrimIlluminRead with default parameters for a single read.
adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
Deprecated.
Use the varargs version. This no longer returns a warning string..
AdapterUtility - Class in picard.analysis
A utility class for matching reads to adapters.
AdapterUtility(List<String>) - Constructor for class picard.analysis.AdapterUtility
 
add(HaplotypeProbabilities) - Method in class picard.fingerprint.Fingerprint
 
add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
Adds a trio to the PedFile keyed by the individual id.
add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Adds the end to this set, if not already added based on physical location
add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
Add a record to the mark queue.
ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
 
ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
 
ADD_PG_TAG_TO_READS - Variable in class picard.sam.util.PGTagArgumentCollection
 
addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Adds a single point of depth at the desired offset into the coverage array.
addBase(int, int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Adds some depth at the desired offset into the coverage array.
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.BaseCalculator
The function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
 
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorCalculator
the function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
 
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
The function by which new loci are "shown" to the calculator
addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
The function by which new loci are "shown" to the calculator
addBaseQHistogram(MetricsFile<WgsMetrics, Integer>) - Method in class picard.analysis.AbstractWgsMetricsCollector
 
AddCommentsToBam - Class in picard.sam
A tool to add comments to a BAM file header.
AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
 
addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
 
addCustomBindings(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
Add any custom freemarker bindings discovered via custom javadoc tags.
addData(ClusterData, BarcodeData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addData(ClusterData, PfData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addData(ClusterData, PositionalData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addDuplicateReadToMetrics(SAMRecord, DuplicationMetrics) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
addEdge(Node, Node) - Method in class picard.util.GraphUtils.Graph
 
addExon(int, int) - Method in class picard.annotation.Gene.Transcript
 
addHaplotype(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeMap
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
addInfo(AbstractLocusInfo<EdgingRecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.FastWgsMetricsCollector
 
addInfo(AbstractLocusInfo<SamLocusIterator.RecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
 
addInfo(AbstractLocusInfo<T>, ReferenceSequence, boolean) - Method in class picard.analysis.AbstractWgsMetricsCollector
Accumulates the data from AbstractLocusInfo in inner structures
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclIndexFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
 
addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.ReadNameParser
 
addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.
addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
 
addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
 
addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
addMetricsToFile(MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Integer>) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
 
addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
addMetricsToFile(MetricsFile<RnaSeqMetrics, Integer>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) - Static method in class picard.vcf.GenotypeConcordance
Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
addNode(Node) - Method in class picard.util.GraphUtils.Graph
 
AddOATag - Class in picard.sam
 
AddOATag() - Constructor for class picard.sam.AddOATag
 
AddOrReplaceReadGroups - Class in picard.sam
Assigns all the reads in a file to a single new read-group.
AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
 
addReadData(ClusterData, int, BaseData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addReadData(ClusterData, int, CbclData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addReadData(ClusterData, int, QualityData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
addReadToLibraryMetrics(SAMRecord, SAMFileHeader, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
ADDRESS_A_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
ADDRESS_B_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
addResults(MatchResults) - Method in class picard.fingerprint.FingerprintResults
 
addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
Adds a row to the scheme
addSingletonToCount(LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
addSnp(Snp) - Method in class picard.fingerprint.HaplotypeBlock
Adds a SNP to the haplotype.
addToLogLikelihoods(Snp, List<Allele>, double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
Adds collected metrics and depth histogram to file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
 
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in interface picard.analysis.WgsMetricsProcessor
Adds result metric's data to input file
addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.WgsMetricsProcessorImpl
 
addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
 
addUmiObservation(String, String) - Method in class picard.sam.markduplicates.UmiMetrics
Add an observation of a UMI to the metrics
addUmiObservationN() - Method in class picard.sam.markduplicates.UmiMetrics
Add an observation of a UMI containing at least one N to the metrics
advance() - Method in class picard.util.AbstractInputParser
 
advanceFile() - Method in class picard.util.BasicInputParser
 
afterExecute(Runnable, Throwable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
 
AG - picard.fingerprint.DiploidGenotype
 
Aligned - picard.sam.ViewSam.AlignmentStatus
 
ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
The total number of aligned reads used to compute the gc bias metrics.
ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
 
ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
 
ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
 
ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
 
ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
 
AlignmentSummaryMetrics - Class in picard.analysis
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
 
AlignmentSummaryMetrics.Category - Enum in picard.analysis
 
AlignmentSummaryMetricsCollector - Class in picard.analysis
 
AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
 
AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector - Class in picard.analysis
 
AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector - Class in picard.analysis
Class that counts reads that match various conditions
All - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
 
All - picard.sam.ViewSam.AlignmentStatus
 
All - picard.sam.ViewSam.PfStatus
 
ALL - picard.sam.markduplicates.CheckDuplicateMarking.Mode
 
ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
ALL_READS - picard.analysis.MetricAccumulationLevel
 
allAlleles - Variable in class picard.vcf.GenotypeConcordance.Alleles
 
ALLELE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ALLELE_A_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
ALLELE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ALLELE_B_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
ALLELE_FRACTION - Variable in class picard.analysis.CollectWgsMetrics
 
ALLELE_FRACTION - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
ALLELE_FRACTION - Variable in class picard.analysis.TheoreticalSensitivityMetrics
The allele fraction which theoretical sensitivity is calculated for.
AlleleBalanceFilter - Class in picard.vcf.filter
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
 
Alleles(OrderedSet<String>, String, String, String, String) - Constructor for class picard.vcf.GenotypeConcordance.Alleles
 
allelesToStringList(List<Allele>) - Static method in class picard.util.LiftoverUtils
This is a utility method that will convert a list of alleles into a list of base strings.
AlleleSubsettingUtils - Class in picard.util
Utilities class containing methods for restricting VariantContext and GenotypesContext objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting.
AlleleSubsettingUtils() - Constructor for class picard.util.AlleleSubsettingUtils
 
ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
 
ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
 
ALLOW_DUPLICATE_READS - Variable in class picard.fingerprint.CrosscheckFingerprints
 
ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
 
ALLOW_MISSING_FIELDS_IN_HEADER - Variable in class picard.vcf.LiftoverVcf
 
ALLOW_MISSING_UMIS - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
 
allVisitedAlignmentsEqual() - Method in class picard.sam.SamComparisonMetric
 
ALSO_IGNORE_DUPLICATES - Variable in class picard.analysis.CollectGcBiasMetrics
 
ALT_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
The alternative base (or it's complement).
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) alternative base that is called as a result of DNA damage.
ALT_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
The number of alt bases observed.
ALT_NAMES - Variable in class picard.sam.CreateSequenceDictionary
 
ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
ALTERNATIVE_SINGLE_END - picard.util.IlluminaUtil.IlluminaAdapterPair
 
altValues() - Static method in enum picard.analysis.artifacts.Transition
Like values(), but ignores the ref:ref "transitions".
AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
 
AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of unique bases covered by the intervals of all amplicons in the amplicon set
ANALYSIS_DIR - Variable in class picard.fastq.BamToBfq
 
ANALYSIS_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version number of the analysis run
ANALYSIS_VERSION_NUMBER - Variable in class picard.arrays.GtcToVcf
 
ANALYSIS_VERSION_NUMBER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
AnnotationException - Exception in picard.annotation
Exception thrown when loading gene annotations.
AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
 
AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
 
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
ARE_EQUAL - Variable in class picard.sam.SamComparisonMetric
Whether or not to consider the two input files equal.
areEqual() - Method in class picard.sam.util.SamComparison
 
areHistogramsEmpty() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
 
ARRAY_TYPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ArraysControlCodesSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
 
ArraysControlInfo - Class in picard.arrays.illumina
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
ArraysControlInfo(String, String, int, int) - Constructor for class picard.arrays.illumina.ArraysControlInfo
 
ArraysVariantCallingDetailMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
 
ArraysVariantCallingSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
 
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
A "nickname" of this artifact, if it is a known error mode.
asList() - Method in class picard.vcf.GenotypeConcordance.Alleles
 
assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
assertPairedMates(SAMRecord, SAMRecord) - Static method in class picard.sam.SamToFastq
 
assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
 
assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Establishes that records returned by this iterator are expected to be in the specified sort order.
assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.
ASSUME_SORT_ORDER - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
ASSUME_SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
 
ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
 
ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
 
ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
 
ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Deprecated.
ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
 
ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
asVcf(ReferenceSequenceFile) - Method in class picard.fingerprint.HaplotypeMap
 
AsyncIterator<T> - Class in picard.util
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
 
AT - picard.fingerprint.DiploidGenotype
 
AT_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
A measure of how undercovered <= 50% GC regions are relative to the mean.
AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
Illumina-style AT dropout metric.
AtoA - picard.analysis.artifacts.Transition
 
AtoC - picard.analysis.artifacts.Transition
 
AtoG - picard.analysis.artifacts.Transition
 
AtomicIterator<T> - Interface in picard.util
Describes
atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
 
atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
 
AtoT - picard.analysis.artifacts.Transition
 
ATTEMPTED_ALLELES - Static variable in class picard.vcf.LiftoverVcf
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
ATTEMPTED_LOCUS - Static variable in class picard.vcf.LiftoverVcf
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
 
ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
 
ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
 
ATTRIBUTES_TO_REVERSE - Variable in class picard.sam.MergeBamAlignment
 
ATTRIBUTES_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.MergeBamAlignment
 
AUTOCALL_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The overall autocall call rate
AUTOCALL_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The date this sample was autocalled
AUTOCALL_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
AUTOCALL_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as determined by Autocall
AUTOCALL_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
AUTOCALL_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether the sample passes QC based on call rate threshold
AUTOCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version of autocall used for calling this sample
AUTOCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
AVG_POS_3PRIME_SOFTCLIP_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The average length of the soft-clipped bases at the 3' end of reads.
awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Blocks until the work is complete.
awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
awaitThreadPoolTermination(String, ThreadPoolExecutorWithExceptions, Duration) - Static method in class picard.util.ThreadPoolExecutorUtil
 
awaitTileProcessingCompletion() - Method in class picard.illumina.SortedBasecallsConverter
 

B

B - picard.illumina.parser.ReadType
 
BAD_ASSAYS_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
BAD_CYCLES - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of instrument cycles in which 80% or more of base calls were no-calls.
BAF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
BafRegressMetrics - Class in picard.arrays
 
BafRegressMetrics() - Constructor for class picard.arrays.BafRegressMetrics
 
BAIT_BIAS_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
BAIT_BIAS_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
BAIT_BIAS_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
BAIT_DESIGN_EFFICIENCY - Variable in class picard.analysis.directed.HsMetrics
The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
BAIT_INTERVALS - Variable in class picard.analysis.directed.CollectHsMetrics
 
BAIT_OFFSET - Variable in class picard.util.BaitDesigner
 
BAIT_SET - Variable in class picard.analysis.directed.HsMetrics
The name of the bait set used in the hybrid selection.
BAIT_SET_NAME - Variable in class picard.analysis.directed.CollectHsMetrics
 
BAIT_SIZE - Variable in class picard.util.BaitDesigner
 
BAIT_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
The number of bases which are localized to one or more baits.
BaitBiasDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
 
BaitBiasSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
 
BaitDesigner - Class in picard.util
Designs baits for hybrid selection!
BaitDesigner() - Constructor for class picard.util.BaitDesigner
 
BaitDesigner.DesignStrategy - Enum in picard.util
Set of possible design strategies for bait design.
BALANCING_WITHOUT_INTERVAL_SUBDIVISION - picard.util.IntervalList.IntervalListScatterMode
A scatter approach that differs from IntervalListScatterMode.INTERVAL_SUBDIVISION in a few ways.
BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW - picard.util.IntervalList.IntervalListScatterMode
bAlleleFreq - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
bam - picard.sam.RevertSam.FileType
 
BamIndexStats - Class in picard.sam
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
BamIndexStats() - Constructor for class picard.sam.BamIndexStats
 
BamToBfq - Class in picard.fastq
Converts a BAM file into a BFQ (binary fastq formatted) file.
BamToBfq() - Constructor for class picard.fastq.BamToBfq
 
BamToBfqWriter - Class in picard.fastq
Deprecated.
BamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.BamToBfqWriter
Deprecated.
 
BamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.BamToBfqWriter
Deprecated.
 
barcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
Barcode - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
Barcode - Static variable in enum picard.illumina.parser.ReadType
 
BARCODE - Variable in class picard.illumina.BarcodeMetric
The barcode (from the set of expected barcodes) for which the following metrics apply.
BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
BARCODE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
Column header for the first barcode sequence (preferred).
BARCODE_DELIMITER - Static variable in class picard.util.IlluminaUtil
 
BARCODE_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
BARCODE_NAME - Variable in class picard.illumina.BarcodeMetric
The barcode name.
BARCODE_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
Column header for the barcode name.
BARCODE_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
BARCODE_POPULATION_STRATEGY - Variable in class picard.illumina.IlluminaBasecallsToSam
 
BARCODE_PREFIXES - Static variable in class picard.illumina.ExtractBarcodesProgram
 
BARCODE_SEQUENCE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
 
BARCODE_TAG - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
 
BARCODE_WITHOUT_DELIMITER - Variable in class picard.illumina.BarcodeMetric
 
barcodeBytes - Variable in class picard.illumina.BarcodeMetric
 
barcodeBytes - Variable in class picard.util.BarcodeEditDistanceQuery
list of barcodes (e.g.
BarcodeEditDistanceQuery - Class in picard.util
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
BarcodeEditDistanceQuery(byte[][], byte[][], byte[][], int, int) - Constructor for class picard.util.BarcodeEditDistanceQuery
 
barcodeExtractor - Variable in class picard.illumina.BasecallsConverter
 
BarcodeExtractor - Class in picard.illumina
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
BarcodeExtractor(Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure, int, int, int, int, DistanceMetric) - Constructor for class picard.illumina.BarcodeExtractor
 
BarcodeExtractor.BarcodeMatch - Class in picard.illumina
Utility class to hang onto data about the best match for a given barcode
BarcodeFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
BarcodeFileFaker() - Constructor for class picard.illumina.parser.fakers.BarcodeFileFaker
 
BarcodeFileReader - Class in picard.illumina.parser.readers
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
BarcodeFileReader(File) - Constructor for class picard.illumina.parser.readers.BarcodeFileReader
 
BarcodeMatch() - Constructor for class picard.illumina.BarcodeExtractor.BarcodeMatch
 
BarcodeMetric - Class in picard.illumina
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
BarcodeMetric() - Constructor for class picard.illumina.BarcodeMetric
This ctor is necessary for when reading metrics from file
BarcodeMetric(String, String, String, String[]) - Constructor for class picard.illumina.BarcodeMetric
 
barcodeRecordWriterMap - Variable in class picard.illumina.BasecallsConverter
 
Barcodes - picard.illumina.parser.IlluminaDataType
 
BARCODES_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
 
barcodeSeqsToString(byte[][]) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(String[]) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeSeqsToString(List<String>) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
barcodeToMetrics - Variable in class picard.illumina.ExtractBarcodesProgram
 
base - Variable in enum picard.analysis.artifacts.Transition.Base
 
base - Variable in class picard.illumina.parser.ParameterizedFileUtil
If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
BaseBclReader - Class in picard.illumina.parser.readers
 
BaseBclReader.CycleData - Class in picard.illumina.parser.readers
 
BaseBclReader.TileData - Class in picard.illumina.parser.readers
 
BaseCalculator - Interface in picard.sam.SamErrorMetric
An interface that can take a collection of bases (provided as SamLocusIterator.RecordAndOffset and SamLocusAndReferenceIterator.SAMLocusAndReference) and generates a ErrorMetric from them.
BaseCallingProgramGroup - Class in picard.cmdline.programgroups
Tools that process sequencing machine data, e.g.
BaseCallingProgramGroup() - Constructor for class picard.cmdline.programgroups.BaseCallingProgramGroup
 
BaseCalls - picard.illumina.parser.IlluminaDataType
 
BASECALLS_DIR - Variable in class picard.illumina.CheckIlluminaDirectory
 
BASECALLS_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
BASECALLS_DIR - Variable in class picard.illumina.ExtractBarcodesProgram
 
BASECALLS_DIR - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
BasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
BasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.BasecallsConverter
Constructs a new BasecallsConverter object.
BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
Interface that defines a writer that will write out OUTPUT_RECORD type objects.
BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
BasecallsConverterBuilder(File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>) - Constructor for class picard.illumina.BasecallsConverterBuilder
Constructs a new builder used for creating BasecallsConverter objects.
baseCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Get the one-based cycle number of the base, taking the direction of the read into account
BaseDistributionByCycleMetrics - Class in picard.analysis
 
BaseDistributionByCycleMetrics() - Constructor for class picard.analysis.BaseDistributionByCycleMetrics
 
BaseErrorAggregation<CALCULATOR extends BaseCalculator> - Class in picard.sam.SamErrorMetric
An interface and implementations for classes that apply a RecordAndOffsetStratifier to put bases into various "bins" and then compute an ErrorMetric on these bases using a BaseErrorCalculator.
BaseErrorAggregation(Supplier<CALCULATOR>, ReadBaseStratification.RecordAndOffsetStratifier) - Constructor for class picard.sam.SamErrorMetric.BaseErrorAggregation
 
BaseErrorCalculator - Class in picard.sam.SamErrorMetric
 
BaseErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.BaseErrorCalculator
 
BaseErrorMetric - Class in picard.sam.SamErrorMetric
An error metric for the errors in bases.
BaseErrorMetric() - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
 
BaseErrorMetric(String, long, long) - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
 
BaseIlluminaDataProvider - Class in picard.illumina.parser
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
BaseIlluminaDataProvider(int, OutputMapping) - Constructor for class picard.illumina.parser.BaseIlluminaDataProvider
 
baseIndexMap - Static variable in enum picard.analysis.artifacts.Transition
 
baseQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the base-quality of the base under consideration
bases - Variable in class picard.illumina.parser.BclData
 
BASES_TO_WRITE - Variable in class picard.fastq.BamToBfq
 
BasicInputParser - Class in picard.util
TextFileParser which reads a single text file.
BasicInputParser(boolean, int, File...) - Constructor for class picard.util.BasicInputParser
Constructor.
BasicInputParser(boolean, int, InputStream...) - Constructor for class picard.util.BasicInputParser
 
BasicInputParser(boolean, File...) - Constructor for class picard.util.BasicInputParser
Constructor.
BasicInputParser(boolean, InputStream...) - Constructor for class picard.util.BasicInputParser
Constructor.
BB - picard.arrays.illumina.IlluminaGenotype
 
BB - picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
 
BB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
 
bci - Variable in class picard.illumina.parser.MultiTileFileUtil
 
BciFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/14/14.
BciFileFaker() - Constructor for class picard.illumina.parser.fakers.BciFileFaker
 
Bcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
BclData - Class in picard.illumina.parser
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
BclData(int[]) - Constructor for class picard.illumina.parser.BclData
 
BclFileFaker - Class in picard.illumina.parser.fakers
 
BclFileFaker() - Constructor for class picard.illumina.parser.fakers.BclFileFaker
 
BclIndexFaker - Class in picard.illumina.parser.fakers
 
BclIndexFaker() - Constructor for class picard.illumina.parser.fakers.BclIndexFaker
 
BclIndexReader - Class in picard.illumina.parser.readers
Annoyingly, there are two different files with extension .bci in NextSeq output.
BclIndexReader(File) - Constructor for class picard.illumina.parser.readers.BclIndexReader
 
bclQualityEvaluationStrategy - Variable in class picard.illumina.ExtractBarcodesProgram
 
BclQualityEvaluationStrategy - Class in picard.illumina.parser.readers
Describes a mechanism for revising and evaluating qualities read from a BCL file.
BclQualityEvaluationStrategy(int) - Constructor for class picard.illumina.parser.readers.BclQualityEvaluationStrategy
 
BclReader - Class in picard.illumina.parser.readers
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
BclReader(File, BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
 
BclReader(List<File>, int[], BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
 
BEAD_SET_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
BEADSET_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
BedToIntervalList - Class in picard.util
 
BedToIntervalList() - Constructor for class picard.util.BedToIntervalList
 
beforeExecute(Thread, Runnable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
 
BestEndMapqPrimaryAlignmentStrategy - Class in picard.sam
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
BestEndMapqPrimaryAlignmentStrategy() - Constructor for class picard.sam.BestEndMapqPrimaryAlignmentStrategy
 
BestMapqPrimaryAlignmentSelectionStrategy - Class in picard.sam
This strategy was designed for TopHat output, but could be of general utility.
BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
 
binnedHomopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.
binnedReadCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into quintiles of read cycle.
BinnedReadCycleStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
 
biSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
the rate of heterogeneity within doubleton sets.
biSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
the rate of homogeneity within doubleton sets.
BLOCK_SIZE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
BOT - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
 
BpmToNormalizationManifestCsv - Class in picard.arrays.illumina
A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
BpmToNormalizationManifestCsv() - Constructor for class picard.arrays.illumina.BpmToNormalizationManifestCsv
 
BREAK_BANDS_AT_MULTIPLES_OF - Variable in class picard.util.IntervalListTools
 
BUFFER_SIZE - Variable in class picard.util.FifoBuffer
 
bufferSize() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.BciFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.BclFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.BclIndexFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.FileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
bufferSize() - Method in class picard.illumina.parser.fakers.PosFileFaker
 
build() - Method in class picard.illumina.BasecallsConverterBuilder
Builds a basecalls converter
build() - Method in interface picard.vcf.processor.VariantProcessor.AccumulatorGenerator
 
build() - Method in class picard.vcf.processor.VariantProcessor.Builder
 
BUILD_37 - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
Build37ExtendedIlluminaManifest - Class in picard.arrays.illumina
A class to represent an 'Extended' Illumina Manifest file.
Build37ExtendedIlluminaManifest(File) - Constructor for class picard.arrays.illumina.Build37ExtendedIlluminaManifest
 
Build37ExtendedIlluminaManifestRecord - Class in picard.arrays.illumina
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
Build37ExtendedIlluminaManifestRecord.Flag - Enum in picard.arrays.illumina
 
Build37ExtendedIlluminaManifestRecordCreator - Class in picard.arrays.illumina
 
BuildBamIndex - Class in picard.sam
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
BuildBamIndex() - Constructor for class picard.sam.BuildBamIndex
 
byHundredMegabaseChunks(List<File>) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of VariantContext
byHundredMegabasePathChunks(List<PicardHtsPath>) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval(List<PicardHtsPath>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of VariantContext
ByIntervalListVariantContextIterator - Class in picard.vcf
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
ByIntervalListVariantContextIterator(VCFFileReader, IntervalList) - Constructor for class picard.vcf.ByIntervalListVariantContextIterator
 
byteArrayToCharArray(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
 
byteArrayToFloat(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
Utility method to convert a byte array to a float value.
byteArrayToInt(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
Utility method to convert an unsigned short to an int.
byteArrayToString(byte[][], String) - Static method in class picard.util.IlluminaUtil
Concatenates all the barcode sequences with BARCODE_DELIMITER
byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
Deprecated.
 
byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
 

C

C - picard.analysis.artifacts.Transition.Base
 
C - picard.illumina.parser.IntensityChannel
 
C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
 
C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == C.
CALCULATE_BY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
CALCULATE_TUMOR_AWARE_RESULTS - Variable in class picard.fingerprint.CrosscheckFingerprints
 
calculateAllGcs(byte[], int, int) - Static method in class picard.analysis.GcBiasUtils
 
calculateDerivedFields() - Method in class picard.analysis.artifacts.ErrorSummaryMetrics
 
calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
 
calculateDerivedFields() - Method in class picard.analysis.MergeableMetricBase
Placeholder method that will calculate the derived fields from the other ones.
calculateDerivedFields() - Method in class picard.analysis.replicates.IndependentReplicateMetric
 
calculateDerivedFields() - Method in class picard.analysis.WgsMetrics
 
calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
 
calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
 
calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
 
calculateDerivedFields() - Method in class picard.sam.DuplicationMetrics
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
calculateDerivedFields() - Method in class picard.sam.markduplicates.UmiMetrics
 
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.BaseErrorMetric
 
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.IndelErrorMetric
 
calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.OverlappingErrorMetric
 
calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
calculateDerivedFields() - Method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
 
calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
Deprecated.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
Calculate the error rate given the raw counts.
calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
Calculate the error rate given the raw counts.
CalculateFingerprintMetrics - Class in picard.fingerprint
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
CalculateFingerprintMetrics() - Constructor for class picard.fingerprint.CalculateFingerprintMetrics
 
calculateFromDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
calculateFromDerivedFields(long) - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) - Static method in class picard.analysis.GcBiasUtils
 
calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
calculateMatchResults(Fingerprint, Fingerprint) - Static method in class picard.fingerprint.FingerprintChecker
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
calculateMatchResults(Fingerprint, Fingerprint, double, double) - Static method in class picard.fingerprint.FingerprintChecker
 
calculateMatchResults(Fingerprint, Fingerprint, double, double, boolean, boolean) - Static method in class picard.fingerprint.FingerprintChecker
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
CalculateReadGroupChecksum - Class in picard.sam
 
CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
 
calculateRefWindowsByGc(int, File, int) - Static method in class picard.analysis.GcBiasUtils
 
calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
calculateSensitivities(int, Histogram<Integer>, Histogram<Integer>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
This is a utility function to calculate the metrics specific to running theoretical sensitivity over several different allele fractions.
calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
Calculates the number of delimiter-separated "words" in a line and sets the value of wordCount
call() - Method in enum picard.analysis.artifacts.Transition
Gets the call for the transition.
CALL_RATE - Variable in class picard.arrays.BafRegressMetrics
The call rate of the sample (number of non-missing genotypes)
CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The overall call rate
CALL_RATE_PF_THRESHOLD - Static variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
 
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The name of the 'call' sample
CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The name of the 'call' sample
CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The state of the 'call' sample (i.e.
CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
 
callAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
 
callAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
 
callAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
 
CallingMetricAccumulator - Class in picard.vcf
Collects variants and generates metrics about them.
CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
 
CallingMetricAccumulator.Result - Class in picard.vcf
 
callState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
callVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
CAN_SKIP - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
canMerge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value
CANNOT_SKIP_FOUND_NO_MC - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
CANNOT_SKIP_FOUND_OQ - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
canSkip() - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
Checks if we can skip the SAM/BAM/CRAM file when reverting origin base qualities and adding mate cigars.
capFromAbove(double[], double) - Static method in class picard.util.MathUtil
Returns the array capped (from above) by the value of top
capFromBelow(double[], double) - Static method in class picard.util.MathUtil
Returns the array capped (from below) by the value of floor
CappedHaplotypeProbabilities - Class in picard.fingerprint
 
CappedHaplotypeProbabilities(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.CappedHaplotypeProbabilities
 
CASAVA_1_8 - picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
 
Casava18ReadNameEncoder - Class in picard.fastq
A read name encoder conforming to the standard described by Illumina Casava 1.8.
Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
 
CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
CATEGORY - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
One of either WHOLE_GENOME or NON_ZERO_REGIONS
CATEGORY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
Grouping categories for controls.
Cbcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
CbclData - Class in picard.illumina.parser
This class provides that data structure for cbcls.
CbclData(int[], int) - Constructor for class picard.illumina.parser.CbclData
 
CbclReader - Class in picard.illumina.parser.readers
------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
CbclReader(List<File>, Map<Integer, File>, int[], int, List<AbstractIlluminaPositionFileReader.PositionInfo>, int[]) - Constructor for class picard.illumina.parser.readers.CbclReader
 
CC - picard.fingerprint.DiploidGenotype
 
CDS_END - picard.annotation.RefFlatReader.RefFlatColumns
 
CDS_START - picard.annotation.RefFlatReader.RefFlatColumns
 
CenteredConstrained - picard.util.BaitDesigner.DesignStrategy
Implementation that "constrains" baits to be within the target region when possible.
CG - picard.fingerprint.DiploidGenotype
 
CHAIN - Variable in class picard.fingerprint.LiftOverHaplotypeMap
 
CHAIN - Variable in class picard.util.LiftOverIntervalList
 
CHAIN - Variable in class picard.vcf.LiftoverVcf
 
CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
 
CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
 
CHART_OUTPUT - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
 
CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
 
CHECK_FIRST_N_RECORDS - Variable in class picard.vcf.FixVcfHeader
 
CheckDuplicateMarking - Class in picard.sam.markduplicates
 
CheckDuplicateMarking() - Constructor for class picard.sam.markduplicates.CheckDuplicateMarking
 
CheckDuplicateMarking.Mode - Enum in picard.sam.markduplicates
 
CheckFingerprint - Class in picard.fingerprint
Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
CheckFingerprint() - Constructor for class picard.fingerprint.CheckFingerprint
 
checkFingerprints(List<Path>, List<Path>, String, boolean) - Method in class picard.fingerprint.FingerprintChecker
Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
checkFingerprintsFromPaths(List<Path>, List<Path>, String, String) - Method in class picard.fingerprint.FingerprintChecker
Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
CheckIlluminaDirectory - Class in picard.illumina
Program to check a lane of an Illumina output directory.
CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
 
checkOutOfBounds(int) - Method in class picard.analysis.CounterManager
Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length CounterManager.readLength.
checkRInstallation(boolean) - Static method in class picard.cmdline.CommandLineProgram
Check if R is installed
CheckTerminatorBlock - Class in picard.sam
Simple class to check the terminator block of a SAM file.
CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
 
checkTileCount() - Method in class picard.illumina.parser.ParameterizedFileUtil
 
checkTileCount() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
 
CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
ChimeraUtil - Class in picard.analysis
 
ChimeraUtil() - Constructor for class picard.analysis.ChimeraUtil
 
CHIMERIC - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
CHIP_TYPE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The chip type name
CHIP_WELL_BARCODE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The chip well barcode of the Illumina array being assayed
CHIP_WELL_BARCODE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
CHROM - Variable in class picard.analysis.FingerprintingDetailMetrics
The chromosome on which the SNP resides.
CHROMOSOME - picard.annotation.RefFlatReader.RefFlatColumns
 
CHROMOSOME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
CigarOperatorsInReadStratifier(CigarOperator) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
 
CircularByteBuffer - Class in picard.util
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
Constructs a buffer capable of holding the given number of bytes.
ClassFinder - Class in picard.cmdline
Utility class that can scan for classes in the classpath and find all the ones annotated with a particular annotation.
ClassFinder() - Constructor for class picard.cmdline.ClassFinder
 
ClassFinder(File) - Constructor for class picard.cmdline.ClassFinder
 
ClassFinder(ClassLoader) - Constructor for class picard.cmdline.ClassFinder
 
CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
 
classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
CleanSam - Class in picard.sam
 
CleanSam() - Constructor for class picard.sam.CleanSam
 
cleanUp() - Method in class picard.util.ThreadPoolExecutorWithExceptions
Calls `shutdownNow, adjusts the core size to 0 and low timeout to ensure threads get killed and garbage collected.
clear() - Method in class picard.analysis.CounterManager
Clears all inner Counter arrays
clear() - Method in class picard.illumina.parser.readers.CbclReader
 
CLEAR_DT - Variable in class picard.sam.markduplicates.MarkDuplicates
 
CLIP_ADAPTERS - Variable in class picard.fastq.BamToBfq
 
CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
 
CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
 
clipForOverlappingReads(SAMRecord, SAMRecord, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
Checks to see whether the ends of the reads overlap and clips reads if necessary.
CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
 
CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
 
CLIPPING_MIN_LENGTH - Variable in class picard.sam.SamToFastq
 
ClippingUtility - Class in picard.util
Utilities to clip the adapter sequence from a SAMRecord read
ClippingUtility() - Constructor for class picard.util.ClippingUtility
 
Clocs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
ClocsFileFaker - Class in picard.illumina.parser.fakers
 
ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
 
ClocsFileReader - Class in picard.illumina.parser.readers
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
 
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
 
clone() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
close() - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
 
close() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
close() - Method in class picard.arrays.illumina.InfiniumEGTFile
 
close() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
close() - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
Closes the writer.
close() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
close() - Method in class picard.illumina.parser.MultiTileFilterParser
 
close() - Method in class picard.illumina.parser.MultiTileLocsParser
 
close() - Method in class picard.illumina.parser.PerTileParser
 
close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
close() - Method in class picard.illumina.parser.readers.BclReader
 
close() - Method in class picard.illumina.parser.readers.CbclReader
 
close() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
close() - Method in class picard.illumina.parser.readers.LocsFileReader
 
close() - Method in class picard.illumina.parser.readers.PosFileReader
 
close() - Method in class picard.sam.AbstractAlignmentMerger
 
close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
close() - Method in class picard.util.AbstractInputParser
Closes this stream and releases any system resources associated with it.
close() - Method in class picard.util.AsyncIterator
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
close() - Method in class picard.util.BasicInputParser
Closes the underlying stream
close() - Method in class picard.util.CircularByteBuffer
Signals that the buffer is closed and no further writes will occur.
close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
close() - Method in class picard.util.TabbedTextFileWithHeaderParser
Release all resources associated with the parser.
close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
close() - Method in class picard.vcf.processor.VariantIteratorProducer
Closes any latent file handles that may have been opened by calls to VariantIteratorProducer.iterators().
closeWriter() - Method in class picard.sam.FixMateInformation
 
closeWriters() - Method in class picard.illumina.BasecallsConverter
Closes all writers.
cluster() - Method in class picard.util.GraphUtils.Graph
returns the cluster map of connected components
CLUSTER - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
The cluster identifier to which the two groups within this metric (CrosscheckMetric.LEFT_GROUP_VALUE and CrosscheckMetric.RIGHT_GROUP_VALUE) belong.
CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
CLUSTER_FILE - Variable in class picard.arrays.GtcToVcf
 
CLUSTER_FILE - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
 
CLUSTER_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
CLUSTER_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
CLUSTER_FILE_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the cluster file used
CLUSTER_ID - picard.illumina.parser.IlluminaMetricsCode
 
CLUSTER_SIZE - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
The number of different groups that are assigned to this cluster.
ClusterCrosscheckMetrics - Class in picard.fingerprint
Summary
ClusterCrosscheckMetrics() - Constructor for class picard.fingerprint.ClusterCrosscheckMetrics
 
ClusterData - Class in picard.illumina.parser
Store the information from Illumina files for a single cluster with one or more reads.
ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
Used for testing, reads is set directly with no copying to the input array
ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
Creates a ClusterData with one read for each type provided
ClusterDataToSamConverter - Class in picard.illumina
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
ClusterDataToSamConverter(String, Map<Integer, String>, ReadStructure, List<AdapterPair>, ClusterDataToSamConverter.PopulateBarcode, boolean) - Constructor for class picard.illumina.ClusterDataToSamConverter
Constructor
ClusteredCrosscheckMetric - Class in picard.fingerprint
A metric class to hold the result of ClusterCrosscheckMetrics fingerprints.
ClusteredCrosscheckMetric() - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
 
ClusteredCrosscheckMetric(CrosscheckMetric) - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
 
clusterVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
code() - Method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
 
CODING - picard.annotation.LocusFunction
 
CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
codingEnd - Variable in class picard.annotation.Gene.Transcript
 
codingStart - Variable in class picard.annotation.Gene.Transcript
 
COLLECT_ALIGNMENT_INFORMATION - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
CollectAlignmentRefArgCollection() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
 
CollectAlignmentSummaryMetrics - Class in picard.analysis
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
CollectAlignmentSummaryMetrics - picard.analysis.CollectMultipleMetrics.Program
 
CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
 
CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection - Class in picard.analysis
 
CollectArraysVariantCallingMetrics - Class in picard.arrays
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectArraysVariantCallingMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics
 
CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics - Class in picard.arrays
 
CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics - Class in picard.arrays
 
CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics - Class in picard.arrays
 
CollectBaseDistributionByCycle - Class in picard.analysis
 
CollectBaseDistributionByCycle - picard.analysis.CollectMultipleMetrics.Program
 
CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
 
CollectDuplicateMetrics - Class in picard.sam.markduplicates
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
CollectDuplicateMetrics() - Constructor for class picard.sam.markduplicates.CollectDuplicateMetrics
 
collectErrorMessages(List<String>, String[]) - Method in class picard.illumina.ExtractBarcodesProgram
 
CollectGcBiasMetrics - Class in picard.analysis
Tool to collect information about GC bias in the reads in a given BAM file.
CollectGcBiasMetrics - picard.analysis.CollectMultipleMetrics.Program
 
CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
 
CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
Metrics produced by the GetHiSeqXPFFailMetrics program.
CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
 
CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum in picard.illumina.quality
 
CollectHsMetrics - Class in picard.analysis.directed
This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.
CollectHsMetrics() - Constructor for class picard.analysis.directed.CollectHsMetrics
 
CollectIlluminaBasecallingMetrics - Class in picard.illumina
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
 
CollectIlluminaLaneMetrics - Class in picard.illumina
CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
 
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
CollectIndependentReplicateMetrics - Class in picard.analysis.replicates
A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
CollectIndependentReplicateMetrics() - Constructor for class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
CollectInsertSizeMetrics - Class in picard.analysis
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
CollectInsertSizeMetrics - picard.analysis.CollectMultipleMetrics.Program
 
CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
 
CollectionStratifier(Collection<ReadBaseStratification.RecordAndOffsetStratifier<?>>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
 
CollectJumpingLibraryMetrics - Class in picard.analysis
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
 
collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure, String, ValidationStringency) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
CollectMultipleMetrics - Class in picard.analysis
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
 
CollectMultipleMetrics.Program - Enum in picard.analysis
 
CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
 
CollectOxoGMetrics - Class in picard.analysis
Class for trying to quantify the CpCG->CpCA error rate.
CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
 
CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
Metrics class for outputs.
CollectQualityYieldMetrics - Class in picard.analysis
Command line program to calculate quality yield metrics
CollectQualityYieldMetrics - picard.analysis.CollectMultipleMetrics.Program
 
CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
 
CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
A set of metrics used to describe the general quality of a BAM file
CollectQualityYieldMetrics.QualityYieldMetricsCollector - Class in picard.analysis
 
CollectRawWgsMetrics - Class in picard.analysis
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap.
CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
 
CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
 
CollectRnaSeqMetrics - Class in picard.analysis
 
CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
 
CollectRrbsMetrics - Class in picard.analysis
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
 
CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection - Class in picard.analysis
 
CollectRrbsMetricsReferenceArgumentCollection() - Constructor for class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
 
CollectSamErrorMetrics - Class in picard.sam.SamErrorMetric
Program to collect error metrics on bases stratified in various ways.
CollectSamErrorMetrics() - Constructor for class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
CollectSequencingArtifactMetrics - picard.analysis.CollectMultipleMetrics.Program
 
CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
CollectTargetedMetrics<METRIC extends MultilevelMetrics,​COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed
Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.
CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
 
CollectTargetedPcrMetrics - Class in picard.analysis.directed
This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.
CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
 
CollectVariantCallingMetrics - Class in picard.vcf
Collects summary and per-sample metrics about variant calls in a VCF file.
CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
 
CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
CollectWgsMetrics - Class in picard.analysis
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
 
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection - Class in picard.analysis
 
CollectWgsMetrics.WgsMetricsCollector - Class in picard.analysis
 
CollectWgsMetricsIntervalArgumentCollection() - Constructor for class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
 
CollectWgsMetricsWithNonZeroCoverage - Class in picard.analysis
 
CollectWgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage - Class in picard.analysis
Metrics for evaluating the performance of whole genome sequencing experiments.
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category - Enum in picard.analysis
 
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector - Class in picard.analysis
 
COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
Implementation note, this is duplicate code stolen from HTSJDK's Default.java /** Decides if we want to write colors to the terminal.
columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
columnLabelsList() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
CombineGenotypingArrayVcfs - Class in picard.arrays
A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
CombineGenotypingArrayVcfs() - Constructor for class picard.arrays.CombineGenotypingArrayVcfs
 
combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
CommandLineDefaults - Class in picard.cmdline
Embodies defaults for global values that affect how the Picard Command Line operates.
CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
 
CommandLineProgram - Class in picard.cmdline
Abstract class to facilitate writing command-line programs.
CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
 
CommandLineSyntaxTranslater - Class in picard.cmdline
Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.
CommandLineSyntaxTranslater() - Constructor for class picard.cmdline.CommandLineSyntaxTranslater
 
COMMENT - Variable in class picard.sam.AddCommentsToBam
 
COMMENT - Variable in class picard.sam.FastqToSam
 
COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
COMMENT - Variable in class picard.sam.MergeSamFiles
 
COMMENT - Variable in class picard.util.IntervalListTools
 
COMMENT - Variable in class picard.vcf.GatherVcfs
 
COMMENT - Variable in class picard.vcf.MergeVcfs
 
compare(int, int) - Static method in class picard.util.MathUtil
 
COMPARE_MQ - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
CompareGtcFiles - Class in picard.arrays.illumina
A simple tool to compare two Illumina GTC files.
CompareGtcFiles() - Constructor for class picard.arrays.illumina.CompareGtcFiles
 
CompareMetrics - Class in picard.analysis
Compare two metrics files.
CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
 
compareMetricValues(Object, Object, String) - Method in class picard.analysis.CompareMetrics
 
CompareSAMs - Class in picard.sam
Rudimentary SAM comparer.
CompareSAMs() - Constructor for class picard.sam.CompareSAMs
 
compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
 
compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
 
compareTo(Gene) - Method in class picard.annotation.Gene
 
compareTo(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeBlock
 
compareTo(MatchResults) - Method in class picard.fingerprint.MatchResults
Provides a natural sort so that better matches (by LOD) sort earlier.
compareTo(Snp) - Method in class picard.fingerprint.Snp
 
compareTo(Pair<X, Y>) - Method in class picard.sam.util.Pair
 
compareTo(PrimaryAlignmentKey) - Method in class picard.sam.util.PrimaryAlignmentKey
 
compareTo(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
CompareVariantContextToLocus(SAMSequenceDictionary, VariantContext, Locus) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
Compares a VariantContext to a Locus providing information regarding possible overlap, or relative location
complement() - Method in enum picard.analysis.artifacts.Transition
Return the complementary transition.
COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractBarcodesProgram
 
COMPRESS_OUTPUTS_PER_RG - Variable in class picard.sam.SamToFastq
 
COMPRESS_OUTPUTS_PER_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
 
COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
 
computeQScore(long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
compute a qscore given the number of errors and the total number of bases.
computeQScore(long, long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
compute a qscore given the number of errors and the total number of bases.
CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
CONCAT - picard.util.IntervalListTools.Action
 
CONCAT_ALL - picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
 
consensusStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratify by tags used during duplex and single index consensus calling.
ConsensusStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
 
contains(Snp) - Method in class picard.fingerprint.HaplotypeBlock
Returns true if the SNP is contained within the haplotype block, false otherwise.
contamination - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
 
CONTAMINATION - Variable in class picard.fingerprint.IdentifyContaminant
 
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The sequence context to which the analysis is constrained.
CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The sequence context being reported on.
CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
 
CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
contig() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
contig() - Method in class picard.vcf.processor.VcfPathSegment
 
CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
CONTINGENCY_STATE_HEADER_LINE - Static variable in class picard.vcf.GenotypeConcordance
 
CONTINGENCY_STATE_TAG - Static variable in class picard.vcf.GenotypeConcordance
 
CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
CONTROL - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
Various control intensities that are present on the infinium chips.
CONTROL_INFO - Static variable in class picard.arrays.illumina.ArraysControlInfo
 
convert(File, File, File, Boolean) - Static method in class picard.sam.SamFormatConverter
Convert a file from one of sam/bam/cram format to another based on the extension of output.
convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.BasecallsConverter.ClusterDataConverter
Creates the OUTPUT_RECORDs from the cluster
convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
Creates the SAMRecord for each read in the cluster
CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
Number of times this CpG site was converted (TG for + strand, CA for - strand)
converter - Variable in class picard.illumina.BasecallsConverter
 
ConvertHaplotypeDatabaseToVcf - Class in picard.fingerprint
 
ConvertHaplotypeDatabaseToVcf() - Constructor for class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
 
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
 
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
 
convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
 
convertPicardStyleToPosixStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
 
ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
 
ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
Converts from Solexa ASCII to Phred binary in place.
copy() - Method in class picard.illumina.BarcodeMetric
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
COPY_TO_TAG - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
copyFromBaseClass(T, S) - Static method in class picard.util.ReflectionUtil
 
CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of aligned reads that are mapped to the correct strand.
correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
correspondingInterval() - Method in class picard.vcf.processor.VcfPathSegment
 
COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
COUNT_OUTPUT - Variable in class picard.util.IntervalListTools
 
COUNT_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics
 
counter - Variable in class picard.analysis.AbstractWgsMetricsCollector
The number of processed genomic bases
CounterManager - Class in picard.analysis
Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
CounterManager(int, int) - Constructor for class picard.analysis.CounterManager
Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method
CounterManager.Counter - Class in picard.analysis
Class represents an integer array with methods to increment and get the values from it with respect to offset of outer CounterManager.
CountingAdapterFilter - Class in picard.filter
Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence
CountingAdapterFilter() - Constructor for class picard.filter.CountingAdapterFilter
 
CountingDuplicateFilter - Class in picard.filter
Counting filter that discards reads that have been marked as duplicates.
CountingDuplicateFilter() - Constructor for class picard.filter.CountingDuplicateFilter
 
CountingFilter - Class in picard.filter
A SamRecordFilter that counts the number of bases in the reads which it filters out.
CountingFilter() - Constructor for class picard.filter.CountingFilter
 
CountingMapQFilter - Class in picard.filter
Counting filter that discards reads below a configurable mapping quality threshold.
CountingMapQFilter(int) - Constructor for class picard.filter.CountingMapQFilter
 
CountingPairedFilter - Class in picard.filter
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
CountingPairedFilter() - Constructor for class picard.filter.CountingPairedFilter
 
COVARIATE - Variable in class picard.sam.SamErrorMetric.ErrorMetric
The value of the covariate define the bases included in this metric
Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
Constructs a new coverage object for the provided mapping with the desired padding either side.
COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
 
COVERAGE_CAP - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
coverageCap - Variable in class picard.analysis.AbstractWgsMetricsCollector
Positions with coverage exceeding this value are treated as if they had coverage at this value
coverageCap - Variable in class picard.analysis.WgsMetrics
The maximum depth/coverage to consider.
CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
 
CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
Number of CpG sites that were converted (TG for +, CA for -)
CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
Number of CpG sites encountered
cram - picard.sam.RevertSam.FileType
 
CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
 
CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
 
CreateBafRegressMetricsFile - Class in picard.arrays
A simple program to create a standard picard metrics file from the output of bafRegress
CreateBafRegressMetricsFile() - Constructor for class picard.arrays.CreateBafRegressMetricsFile
 
createBarcodeExtractor() - Method in class picard.illumina.ExtractBarcodesProgram
 
CreateExtendedIlluminaManifest - Class in picard.arrays.illumina
Create an Extended Illumina Manifest by performing a liftover to Build 37.
CreateExtendedIlluminaManifest() - Constructor for class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
Soft-clip an alignment that hangs off the end of its reference sequence.
createRecord(IlluminaManifestRecord) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
createSamFileHeader() - Method in class picard.sam.FastqToSam
Creates a simple header with the values provided on the command line.
createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
 
CreateSeqDictReferenceArgumentCollection() - Constructor for class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
 
CreateSequenceDictionary - Class in picard.sam
Create a SAM/BAM file from a fasta containing reference sequence.
CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
 
CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection - Class in picard.sam
 
createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
createVCSetFromFingerprint(Fingerprint, ReferenceSequenceFile, String) - Static method in class picard.fingerprint.FingerprintUtils
A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
CreateVerifyIDIntensityContaminationMetricsFile - Class in picard.arrays
A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
CreateVerifyIDIntensityContaminationMetricsFile() - Constructor for class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
 
createWorkUnit(DocumentedFeature, ClassDoc, Class<?>) - Method in class picard.util.help.PicardHelpDoclet
 
CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
CROSSCHECK_BY - Variable in class picard.fingerprint.CrosscheckFingerprints
 
CROSSCHECK_LIBRARIES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
CROSSCHECK_MODE - Variable in class picard.fingerprint.CrosscheckFingerprints
 
CROSSCHECK_SAMPLES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
CrosscheckFingerprints - Class in picard.fingerprint
Checks that all data in the set of input files appear to come from the same individual.
CrosscheckFingerprints() - Constructor for class picard.fingerprint.CrosscheckFingerprints
 
CrosscheckMetric - Class in picard.fingerprint
A class to hold the result of crosschecking fingerprints.
CrosscheckMetric() - Constructor for class picard.fingerprint.CrosscheckMetric
 
CrosscheckMetric.DataType - Enum in picard.fingerprint
 
CrosscheckMetric.FingerprintResult - Enum in picard.fingerprint
 
CrosscheckReadGroupFingerprints - Class in picard.fingerprint
Deprecated.
6/6/2017 Use CrosscheckFingerprints instead.
CrosscheckReadGroupFingerprints() - Constructor for class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
CsvInputParser - Class in picard.util
 
CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
Constructor
CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
Constructor
CT - picard.fingerprint.DiploidGenotype
 
CtoA - picard.analysis.artifacts.Transition
 
CtoC - picard.analysis.artifacts.Transition
 
CtoG - picard.analysis.artifacts.Transition
 
CtoT - picard.analysis.artifacts.Transition
 
currentReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
The name of the amplicon set used in this metrics collection run
CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
 
customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
customCommandLineValidation() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
customCommandLineValidation() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectBaseDistributionByCycle
 
customCommandLineValidation() - Method in class picard.analysis.CollectGcBiasMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectRnaSeqMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
 
customCommandLineValidation() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
customCommandLineValidation() - Method in class picard.analysis.CompareMetrics
 
customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
customCommandLineValidation() - Method in class picard.analysis.MeanQualityByCycle
 
customCommandLineValidation() - Method in class picard.analysis.QualityScoreDistribution
 
customCommandLineValidation() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
 
customCommandLineValidation() - Method in class picard.arrays.GtcToVcf
 
customCommandLineValidation() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.fastq.BamToBfq
 
customCommandLineValidation() - Method in class picard.fingerprint.CheckFingerprint
 
customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckFingerprints
 
customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
 
customCommandLineValidation() - Method in class picard.illumina.ExtractBarcodesProgram
Parses all barcodes from input files and validates all barcodes are the same length and unique
customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
 
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
 
customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
 
customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
customCommandLineValidation() - Method in class picard.sam.AddOrReplaceReadGroups
 
customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
Use reference filename to create URI to go into header if URI was not passed on cmd line.
customCommandLineValidation() - Method in class picard.sam.DownsampleSam
 
customCommandLineValidation() - Method in class picard.sam.FastqToSam
 
customCommandLineValidation() - Method in class picard.sam.FilterSamReads
 
customCommandLineValidation() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
 
customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
 
customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
 
customCommandLineValidation() - Method in class picard.sam.RevertSam
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
customCommandLineValidation() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
customCommandLineValidation() - Method in class picard.sam.SamToFastq
Put any custom command-line validation in an override of this method.
customCommandLineValidation() - Method in class picard.sam.SamToFastqWithTags
 
customCommandLineValidation() - Method in class picard.sam.SplitSamByNumberOfReads
 
customCommandLineValidation() - Method in class picard.sam.ValidateSamFile
 
customCommandLineValidation() - Method in class picard.sam.ViewSam
 
customCommandLineValidation() - Method in class picard.util.BaitDesigner
 
customCommandLineValidation() - Method in class picard.util.IntervalListTools
 
customCommandLineValidation() - Method in class picard.vcf.FixVcfHeader
 
customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
 
customCommandLineValidation() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability
cycle - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
 
CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil
 

D

DATA_TYPE - Variable in class picard.fingerprint.CrosscheckMetric
 
DATA_TYPES - Variable in class picard.illumina.CheckIlluminaDirectory
 
DATA_TYPES_WITH_BARCODE - Static variable in class picard.illumina.BasecallsConverter
 
DATA_TYPES_WITHOUT_BARCODE - Static variable in class picard.illumina.BasecallsConverter
 
dataFile - Variable in class picard.illumina.parser.MultiTileFileUtil
 
dateCreated - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
DB_SNP - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
DB_SNP - Variable in class picard.analysis.CollectMultipleMetrics
 
DB_SNP - Variable in class picard.analysis.CollectOxoGMetrics
 
DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics
 
DBSNP_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
DBSNP_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Insertion/Deletion ratio of the indel calls made at dbSNP sites
DBSNP_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
DbSnpBitSets() - Constructor for class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
DbSnpBitSetUtil - Class in picard.util
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for all variant types.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for the given variant types.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor.
DbSnpBitSetUtil(Path, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for all variant types.
DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for the given variant types.
DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
Constructor.
DbSnpBitSetUtil.DbSnpBitSets - Class in picard.util
Little tuple class to contain one bitset for SNPs and another for Indels.
DEBUG_FREQUENCY - Variable in class picard.util.FifoBuffer
 
decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
 
decode() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
deduceIdealSplitWeight(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
A method that determines the ideal target "weight" of the output IntervalList.
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
 
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
 
deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
 
deepCopy() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilities
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
DEFAULT_ADAPTER_LENGTH - Static variable in class picard.util.AdapterMarker
 
DEFAULT_ADAPTER_SEQUENCE - Static variable in class picard.analysis.AdapterUtility
 
DEFAULT_BIG_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
DEFAULT_EXPECTED_ORIENTATIONS - Static variable in class picard.analysis.ChimeraUtil
 
DEFAULT_GENOTYPING_ERROR_RATE - Static variable in class picard.fingerprint.FingerprintChecker
 
DEFAULT_INSERT_SIZE_LIMIT - Static variable in class picard.analysis.ChimeraUtil
 
DEFAULT_MAX_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
DEFAULT_MINIMUM_BASE_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
 
DEFAULT_MINIMUM_MAPPING_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
 
DEFAULT_NUM_ADAPTERS_TO_KEEP - Static variable in class picard.util.AdapterMarker
 
DEFAULT_OPTICAL_DUPLICATE_DISTANCE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Static variable in class picard.util.AdapterMarker
 
DEFAULT_QUEUE_SIZE - Static variable in class picard.util.AsyncIterator
 
DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.util.ReadNameParser
The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location.
DEFAULT_TAGS_TO_DROP - Static variable in class picard.util.LiftoverUtils
 
DEFAULT_TAGS_TO_REVERSE - Static variable in class picard.util.LiftoverUtils
Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
defaultEndBiasBases - Static variable in class picard.analysis.directed.RnaSeqMetricsCollector
 
DefaultSkipEmptyFiles - Static variable in class picard.illumina.parser.ParameterizedFileUtil
 
DEFINITE_GENOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold
deletion - picard.util.VariantType
 
DELETIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The (phred) rate of deletions.
deletionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratify by Deletions in the read cigars.
DelimitedTextFileWithHeaderIterator - Class in picard.util
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
DelimitedTextFileWithHeaderIterator(BasicInputParser) - Constructor for class picard.util.DelimitedTextFileWithHeaderIterator
 
DelimitedTextFileWithHeaderIterator.Row - Class in picard.util
 
demultiplex - Variable in class picard.illumina.BasecallsConverter
 
DENSITY_ID - picard.illumina.parser.IlluminaMetricsCode
 
DepthFilter - Class in picard.vcf.filter
Filters out a record if all variant samples have depth lower than the given value.
DepthFilter(int) - Constructor for class picard.vcf.filter.DepthFilter
 
DESCRIPTION - Variable in class picard.sam.FastqToSam
 
descriptors - Variable in class picard.illumina.parser.ReadStructure
 
DESIGN_NAME - Variable in class picard.util.BaitDesigner
 
DESIGN_ON_TARGET_STRAND - Variable in class picard.util.BaitDesigner
 
DESIGN_STRATEGY - Variable in class picard.util.BaitDesigner
 
DETAIL_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
DETAIL_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
 
DETAILED_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
detailedMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
DETAILS - Variable in class picard.metrics.GcBiasMetrics
 
determineFormats(Set<IlluminaDataType>, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
determineQualityFormat(FastqReader, FastqReader, FastqQualityFormat) - Static method in class picard.sam.FastqToSam
Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
determineState(VariantContext, String, VariantContext, String, int, int, Boolean) - Static method in class picard.vcf.GenotypeConcordance
A method to determine the truth and call states for a pair of variant contexts representing truth and call.
DEV_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
DEV_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
DEV_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
DEV_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
DEVIATIONS - Variable in class picard.analysis.CollectInsertSizeMetrics
 
devR - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
devTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
DiagnosticsAndQCProgramGroup - Class in picard.cmdline.programgroups
Tools that collect sequencing quality-related and comparative metrics
DiagnosticsAndQCProgramGroup() - Constructor for class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
 
DiploidGenotype - Enum in picard.fingerprint
A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
DiploidHaplotype - Enum in picard.fingerprint
Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
DISABLE_SORT - Variable in class picard.vcf.LiftoverVcf
 
DISAGREES_WITH_REF_AND_MATE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
DISAGREES_WITH_REFERENCE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The (phred) rate of bases that disagree with the reference, but agree with their mate
DISCORDANT - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
DISCRIMINATORY_POWER - Variable in class picard.fingerprint.FingerprintMetrics
The difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes.
DiskBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
DiskBasedReadEndsForMarkDuplicatesMap(int, ReadEndsForMarkDuplicatesCodec) - Constructor for class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
distance(BarcodeEditDistanceQuery) - Method in enum picard.illumina.DistanceMetric
 
DISTANCE_MODE - Variable in class picard.illumina.ExtractBarcodesProgram
 
distance0(SingleBarcodeDistanceMetric) - Method in enum picard.illumina.DistanceMetric
 
DistanceMetric - Enum in picard.illumina
 
divide(double[], double[]) - Static method in class picard.util.MathUtil
Calculates the ratio of two arrays of the same length.
divide(double, double) - Static method in class picard.util.MathUtil
Divide two Doubles but return 0.0 if the denominator is 0
DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.GtcToVcf
 
DO_NOT_CHANGE - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
DO_NOT_CHANGE_INVALID - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
DOC_CAT_BASE_CALLING - Static variable in class picard.util.help.HelpConstants
Definition of the group names / descriptions for documentation/help purposes.
DOC_CAT_BASE_CALLING_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_DIAGNOSTICS_AND_QC - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_INTERVALS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_INTERVALS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_METRICS - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_METRICS_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_OTHER - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_OTHER_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_READ_DATA_MANIPULATION - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_READ_DATA_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_REFERENCE - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_REFERENCE_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_TEST - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_TEST_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_EVALUATION - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_EVALUATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_FILTERING - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_FILTERING_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_MANIPULATION - Static variable in class picard.util.help.HelpConstants
 
DOC_CAT_VARIANT_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
 
DOC_SUPERCAT_EXCLUDE - Static variable in class picard.util.help.HelpConstants
 
DOC_SUPERCAT_TOOLS - Static variable in class picard.util.help.HelpConstants
List of "supercategory" values used for doc purposes.
DOC_SUPERCAT_UTILITIES - Static variable in class picard.util.help.HelpConstants
 
DONT_MERGE_ABUTTING - Variable in class picard.util.IntervalListTools
 
DontTag - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
 
doPaired(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
More complicated method that takes two fastq files and builds pairing information in the SAM.
doUnpaired(FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
Creates a simple SAM file from a single fastq file.
DownsampleSam - Class in picard.sam
Summary
DownsampleSam() - Constructor for class picard.sam.DownsampleSam
 
doWork() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
doWork() - Method in class picard.analysis.CollectJumpingLibraryMetrics
Calculates the detailed statistics about the jumping library and then generates the results.
doWork() - Method in class picard.analysis.CollectMultipleMetrics
 
doWork() - Method in class picard.analysis.CollectOxoGMetrics
 
doWork() - Method in class picard.analysis.CollectRrbsMetrics
 
doWork() - Method in class picard.analysis.CollectWgsMetrics
 
doWork() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
doWork() - Method in class picard.analysis.CompareMetrics
 
doWork() - Method in class picard.analysis.directed.CollectTargetedMetrics
Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
doWork() - Method in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
doWork() - Method in class picard.analysis.SinglePassSamProgram
Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
doWork() - Method in class picard.annotation.SortGff
 
doWork() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
 
doWork() - Method in class picard.arrays.CombineGenotypingArrayVcfs
 
doWork() - Method in class picard.arrays.CreateBafRegressMetricsFile
 
doWork() - Method in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
 
doWork() - Method in class picard.arrays.GtcToVcf
 
doWork() - Method in class picard.arrays.illumina.BpmToNormalizationManifestCsv
 
doWork() - Method in class picard.arrays.illumina.CompareGtcFiles
 
doWork() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
doWork() - Method in class picard.arrays.MergePedIntoVcf
 
doWork() - Method in class picard.arrays.VcfToAdpc
 
doWork() - Method in class picard.cmdline.CommandLineProgram
Do the work after command line has been parsed.
doWork() - Method in class picard.fastq.BamToBfq
 
doWork() - Method in class picard.fingerprint.CalculateFingerprintMetrics
 
doWork() - Method in class picard.fingerprint.CheckFingerprint
 
doWork() - Method in class picard.fingerprint.ClusterCrosscheckMetrics
 
doWork() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
 
doWork() - Method in class picard.fingerprint.CrosscheckFingerprints
 
doWork() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
doWork() - Method in class picard.fingerprint.ExtractFingerprint
 
doWork() - Method in class picard.fingerprint.IdentifyContaminant
 
doWork() - Method in class picard.fingerprint.LiftOverHaplotypeMap
 
doWork() - Method in class picard.illumina.CheckIlluminaDirectory
 
doWork() - Method in class picard.illumina.CollectIlluminaBasecallingMetrics
 
doWork() - Method in class picard.illumina.CollectIlluminaLaneMetrics
 
doWork() - Method in class picard.illumina.ExtractIlluminaBarcodes
 
doWork() - Method in class picard.illumina.IlluminaBasecallsToFastq
 
doWork() - Method in class picard.illumina.IlluminaBasecallsToSam
 
doWork() - Method in class picard.illumina.MarkIlluminaAdapters
 
doWork() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
doWork() - Method in class picard.reference.ExtractSequences
 
doWork() - Method in class picard.reference.NonNFastaSize
 
doWork() - Method in class picard.reference.NormalizeFasta
 
doWork() - Method in class picard.sam.AddCommentsToBam
 
doWork() - Method in class picard.sam.AddOATag
 
doWork() - Method in class picard.sam.AddOrReplaceReadGroups
 
doWork() - Method in class picard.sam.BamIndexStats
Main method for the program.
doWork() - Method in class picard.sam.BuildBamIndex
Main method for the program.
doWork() - Method in class picard.sam.CalculateReadGroupChecksum
 
doWork() - Method in class picard.sam.CheckTerminatorBlock
 
doWork() - Method in class picard.sam.CleanSam
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CompareSAMs
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.CreateSequenceDictionary
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.DownsampleSam
 
doWork() - Method in class picard.sam.FastqToSam
 
doWork() - Method in class picard.sam.FilterSamReads
 
doWork() - Method in class picard.sam.FixMateInformation
 
doWork() - Method in class picard.sam.GatherBamFiles
 
doWork() - Method in class picard.sam.markduplicates.CheckDuplicateMarking
 
doWork() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
Method that does most of the work.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicates
Main work method.
doWork() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
Main work method.
doWork() - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
Main work method.
doWork() - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
doWork() - Method in class picard.sam.MergeBamAlignment
 
doWork() - Method in class picard.sam.MergeSamFiles
Combines multiple SAM/BAM/CRAM files into one.
doWork() - Method in class picard.sam.PositionBasedDownsampleSam
 
doWork() - Method in class picard.sam.ReorderSam
 
doWork() - Method in class picard.sam.ReplaceSamHeader
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
doWork() - Method in class picard.sam.RevertSam
 
doWork() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
doWork() - Method in class picard.sam.SamFormatConverter
 
doWork() - Method in class picard.sam.SamToFastq
 
doWork() - Method in class picard.sam.SetNmMdAndUqTags
 
doWork() - Method in class picard.sam.SortSam
 
doWork() - Method in class picard.sam.SplitSamByLibrary
 
doWork() - Method in class picard.sam.SplitSamByNumberOfReads
 
doWork() - Method in class picard.sam.ValidateSamFile
Do the work after command line has been parsed.
doWork() - Method in class picard.sam.ViewSam
 
doWork() - Method in class picard.util.AccumulateQualityYieldMetrics
 
doWork() - Method in class picard.util.BaitDesigner
 
doWork() - Method in class picard.util.BedToIntervalList
 
doWork() - Method in class picard.util.FifoBuffer
 
doWork() - Method in class picard.util.IntervalListToBed
 
doWork() - Method in class picard.util.IntervalListTools
 
doWork() - Method in class picard.util.LiftOverIntervalList
Do the work after command line has been parsed.
doWork() - Method in class picard.util.ScatterIntervalsByNs
 
doWork() - Method in class picard.vcf.AccumulateVariantCallingMetrics
 
doWork() - Method in class picard.vcf.CollectVariantCallingMetrics
 
doWork() - Method in class picard.vcf.filter.FilterVcf
 
doWork() - Method in class picard.vcf.FixVcfHeader
 
doWork() - Method in class picard.vcf.GatherVcfs
 
doWork() - Method in class picard.vcf.GenotypeConcordance
 
doWork() - Method in class picard.vcf.LiftoverVcf
 
doWork() - Method in class picard.vcf.MakeSitesOnlyVcf
 
doWork() - Method in class picard.vcf.MakeVcfSampleNameMap
 
doWork() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
 
doWork() - Method in class picard.vcf.MergeVcfs
 
doWork() - Method in class picard.vcf.RenameSampleInVcf
 
doWork() - Method in class picard.vcf.SortVcf
 
doWork() - Method in class picard.vcf.SplitVcfs
 
doWork() - Method in class picard.vcf.UpdateVcfSequenceDictionary
 
doWork() - Method in class picard.vcf.VcfFormatConverter
 
doWork() - Method in class picard.vcf.VcfToIntervalList
 
draw() - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
 
DROP_MISSING_CONTIGS - Variable in class picard.util.BedToIntervalList
 
DUAL_INDEXED - picard.util.IlluminaUtil.IlluminaAdapterPair
 
DUPE - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
The record passes validation but is a duplicate (another assay at the same locus with the same alleles)
DUPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
DUPLEX_CONSENSUS - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Consensus read which has two or more observations in both directions.
DUPLEX_SINGLETON - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Read which has two observations, one from each direction.
DUPLEX_UMI - Variable in class picard.sam.markduplicates.MarkDuplicates
 
DUPLICATE_MARKINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
The number of primary records for which duplicate markings are different.
DUPLICATE_SCORING_STRATEGY - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
DUPLICATE_SET_INDEX_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set
DUPLICATE_SET_SIZE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
The attribute in the SAM/BAM file used to store the size of a duplicate set
DUPLICATE_SETS_IGNORING_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
Number of duplicate sets found before taking UMIs into account
DUPLICATE_SETS_WITH_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
Number of duplicate sets found after taking UMIs into account
DUPLICATE_TYPE_LIBRARY - Static variable in class picard.sam.markduplicates.MarkDuplicates
The duplicate type tag value for duplicate type: library.
DUPLICATE_TYPE_SEQUENCING - Static variable in class picard.sam.markduplicates.MarkDuplicates
The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").
DUPLICATE_TYPE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
The optional attribute in SAM/BAM/CRAM files used to store the duplicate type.
duplicateSetSize - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
DuplicationMetrics - Class in picard.sam
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
DuplicationMetrics() - Constructor for class picard.sam.DuplicationMetrics
 
dynamic - picard.sam.RevertSam.FileType
 

E

EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in picard.sam
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
 
EmpiricalPhasingMetricsOutReader - Class in picard.illumina.parser.readers
 
EmpiricalPhasingMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
 
EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics - Class in picard.illumina.parser.readers
 
EMPTY - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
 
EMPTY - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
EMPTY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
EMPTY_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The empty (no contingency info) count across all variants
EmptyOutputArgumentCollection - Class in picard.cmdline.argumentcollections
 
EmptyOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
 
encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
 
encode(RepresentativeReadIndexer) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
encodeDictionary(BufferedWriter, Iterator<SAMSequenceRecord>) - Static method in class picard.util.SequenceDictionaryUtils
Encodes a sequence dictionary
encodeMappingInformation(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
Encodes mapping information from a record into a string according to the format sepcified in the Sam-Spec under the SA tag.
end - Variable in class picard.annotation.Gene.Transcript.Exon
 
end - Variable in class picard.illumina.parser.Range
 
end() - Method in class picard.annotation.Gene.Transcript
 
END_BIAS_BASES - Variable in class picard.analysis.CollectRnaSeqMetrics
 
ENFORCE_SAME_SAMPLES - Variable in class picard.vcf.FixVcfHeader
 
equals(Object) - Method in class picard.annotation.Gene
 
equals(Object) - Method in class picard.annotation.Gene.Transcript
 
equals(Object) - Method in class picard.fingerprint.FingerprintIdDetails
 
equals(Object) - Method in class picard.fingerprint.HaplotypeBlock
 
equals(Object) - Method in class picard.fingerprint.Snp
 
equals(Object) - Method in class picard.illumina.parser.Range
 
equals(Object) - Method in class picard.illumina.parser.ReadDescriptor
 
equals(Object) - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
 
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
equals(Object) - Method in class picard.illumina.parser.ReadStructure
 
equals(Object) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
equals(Object) - Method in class picard.sam.util.Pair
Calculate whether this pair object is equal to another object.
equals(Object) - Method in class picard.sam.util.PrimaryAlignmentKey
 
equals(Object) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
ERROR_BAR_WIDTH - Variable in class picard.analysis.GcBiasDetailMetrics
The radius of error bars in this bin based on the number of observations made.
ERROR_BASES - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
The number of bases that disagree with the reference
ERROR_METRICS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The estimated error rate due to this artifact.
ERROR_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
ERROR_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
ErrorMetric - Class in picard.sam.SamErrorMetric
Created by farjoun on 6/26/18.
ErrorMetric() - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
 
ErrorMetric(String, long) - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
 
ErrorSummaryMetrics - Class in picard.analysis.artifacts
Summary metrics produced by CollectSequencingArtifactMetrics as a roll up of the context-specific error rates, to provide global error rates per type of base substitution.
ErrorSummaryMetrics() - Constructor for class picard.analysis.artifacts.ErrorSummaryMetrics
 
escapePeriods(String) - Static method in class picard.illumina.parser.ParameterizedFileUtil
Escape the period character.
ESTIMATE - Variable in class picard.arrays.BafRegressMetrics
The estimate of contamination from the model (on the 0.0-1.0 scale)
ESTIMATED_LIBRARY_SIZE - Variable in class picard.sam.DuplicationMetrics
The estimated number of unique molecules in the library based on PE duplication.
EstimateLibraryComplexity - Class in picard.sam.markduplicates
Attempts to estimate library complexity from sequence alone.
EstimateLibraryComplexity() - Constructor for class picard.sam.markduplicates.EstimateLibraryComplexity
 
estimateLibrarySize(long, long) - Static method in class picard.sam.DuplicationMetrics
Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
estimateRoi(long, double, long, long) - Static method in class picard.sam.DuplicationMetrics
Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
exception - Variable in class picard.util.ThreadPoolExecutorWithExceptions
 
excludeAligned - picard.sam.FilterSamReads.Filter
 
excludeReadList - picard.sam.FilterSamReads.Filter
 
excludeTagValues - picard.sam.FilterSamReads.Filter
 
excludingNonOverlaps(VcfFileSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
Deprecated.
Returns a decorated VcfFileSegmentGenerator that filters out VcfFileSegments that have no overlap with the provided OverlapDetector.
excludingNonOverlaps(VcfPathSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
Returns a decorated VcfPathSegmentGenerator that filters out VcfPathSegments that have no overlap with the provided OverlapDetector.
executeFromClasspath(String, String...) - Static method in class picard.util.RExecutor
Executes the given R script that is stored in a file on the classpath.
executeFromFile(File, String...) - Static method in class picard.util.RExecutor
Executes the given R script that is stored in a file by a call to Rscript.
EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE - Static variable in class picard.vcf.LiftoverVcf
 
EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND - Variable in class picard.fingerprint.CheckFingerprint
 
EXIT_CODE_WHEN_MISMATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
 
EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CheckFingerprint
 
EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CrosscheckFingerprints
 
Exon(int, int) - Constructor for class picard.annotation.Gene.Transcript.Exon
 
EXON_COUNT - picard.annotation.RefFlatReader.RefFlatColumns
 
EXON_ENDS - picard.annotation.RefFlatReader.RefFlatColumns
 
EXON_STARTS - picard.annotation.RefFlatReader.RefFlatColumns
 
exons - Variable in class picard.annotation.Gene.Transcript
 
EXP_CLUSTERS_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
EXPECT_ALL_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
 
EXPECT_ALL_READ_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
Deprecated.
 
EXPECTED_GENDER - Variable in class picard.arrays.GtcToVcf
 
EXPECTED_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
EXPECTED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
The expected genotype of the sample at the SNP locus.
EXPECTED_HET - Variable in class picard.fingerprint.FingerprintMetrics
Expected number of heterozygous calls
EXPECTED_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
Expected number of major allele homozygous calls
EXPECTED_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
Expected number of major allele homozygous calls
EXPECTED_INSERT_SIZE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
EXPECTED_MATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
 
EXPECTED_MISMATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
 
EXPECTED_ORIENTATIONS - Variable in class picard.sam.MergeBamAlignment
 
EXPECTED_PAIR_ORIENTATIONS - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
EXPECTED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
 
EXPECTED_VERSION - Static variable in class picard.illumina.parser.readers.FilterFileReader
Expected Version
EXTENDED_ILLUMINA_MANIFEST - Variable in class picard.arrays.GtcToVcf
 
EXTENDED_ILLUMINA_MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
EXTENDED_ILLUMINA_MANIFEST_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
EXTENDED_MANIFEST_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version of the Extended Illumina Manifest used for calling this sample
extendedIterator() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
 
extension - Variable in class picard.illumina.parser.ParameterizedFileUtil
The file extension for this class, file extension does not have the standard meaning in this instance.
EXTENSION - Static variable in class picard.arrays.illumina.InfiniumEGTFile
 
EXTRA_ARGUMENT - Variable in class picard.analysis.CollectMultipleMetrics
 
EXTRACT_CONTAMINATED - Variable in class picard.fingerprint.IdentifyContaminant
 
EXTRACT_CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
 
ExtractBarcodesProgram - Class in picard.illumina
 
ExtractBarcodesProgram() - Constructor for class picard.illumina.ExtractBarcodesProgram
 
ExtractFingerprint - Class in picard.fingerprint
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
ExtractFingerprint() - Constructor for class picard.fingerprint.ExtractFingerprint
 
ExtractIlluminaBarcodes - Class in picard.illumina
Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes() - Constructor for class picard.illumina.ExtractIlluminaBarcodes
 
ExtractIlluminaBarcodes.PerTileBarcodeExtractor - Class in picard.illumina
Extracts barcodes and accumulates metrics for an entire tile.
ExtractSequences - Class in picard.reference
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
ExtractSequences() - Constructor for class picard.reference.ExtractSequences
 

F

F - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
F1F2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
 
F1R2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
 
F2R1 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
 
FAIL_REF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
 
fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
 
fakeBciFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.BclIndexFaker
 
fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclIndexFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
 
fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
fakeMultiTileBclFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
FAMILY_ID - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The family ID assigned to the trio for which these metrics are calculated.
FASTQ - Variable in class picard.sam.FastqToSam
 
FASTQ - Variable in class picard.sam.SamToFastq
 
FASTQ2 - Variable in class picard.sam.FastqToSam
 
FastqToSam - Class in picard.sam
Converts a FASTQ file to an unaligned BAM or SAM file.
FastqToSam() - Constructor for class picard.sam.FastqToSam
 
FastWgsMetricsCollector - Class in picard.analysis
Class represents fast algorithm for collecting data from AbstractLocusInfo with a list of aligned EdgingRecordAndOffset objects.
FastWgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.FastWgsMetricsCollector
Creates a collector and initializes the inner data structures
FATHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The ID of the father within the trio.
Female - picard.pedigree.Sex
 
FEMALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
FifoBuffer - Class in picard.util
Summary
FifoBuffer() - Constructor for class picard.util.FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
FILE - picard.fingerprint.CrosscheckMetric.DataType
 
FILE_EXTENSION - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
FILE_EXTENSION - Variable in class picard.analysis.CollectMultipleMetrics
 
FILE_EXTENSION - Static variable in class picard.arrays.CreateBafRegressMetricsFile
 
FILE_EXTENSION - Static variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
 
FILE_EXTENSION - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
FILE_NAME_PATTERN - Static variable in class picard.illumina.parser.BaseIlluminaDataProvider
 
FileFaker - Class in picard.illumina.parser.fakers
 
FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
 
filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
Determine whether or not files are available
filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
 
filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
fileToTile(String) - Static method in class picard.illumina.parser.BaseIlluminaDataProvider
 
fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
Returns only lane and tile information as PerTileFt's do not have End information.
FILL_POOLS - Variable in class picard.util.BaitDesigner
 
filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
 
filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
 
filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
 
filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
Check to see if the VariantContext should have a filter applied to it.
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
 
filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
Test whether or not the genotype should be filtered out.
filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
 
Filter - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
FILTER - Variable in class picard.sam.FilterSamReads
 
FILTER_CANNOT_LIFTOVER_REV_COMP - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_INDEL_STRADDLES_TWO_INTERVALS - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.
FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
 
FILTER_NO_TARGET - Static variable in class picard.vcf.LiftoverVcf
Filter name to use when a target cannot be lifted over.
FILTER_UNPAIRED_READS - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
FilterApplyingVariantIterator - Class in picard.vcf.filter
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of indels that are filtered
FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of SNPs that are filtered
FilterFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
 
FilterFileReader - Class in picard.illumina.parser.readers
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
 
filterOut(SAMRecord) - Method in class picard.filter.CountingFilter
 
filterOut(SAMRecord, SAMRecord) - Method in class picard.filter.CountingFilter
 
FilterSamReads - Class in picard.sam
Summary
FilterSamReads() - Constructor for class picard.sam.FilterSamReads
 
FilterSamReads.Filter - Enum in picard.sam
 
filterSuspectSites() - Method in class picard.fingerprint.Fingerprint
Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
FilterVcf - Class in picard.vcf.filter
Applies a set of hard filters to Variants and to Genotypes within a VCF.
FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
Constructor to default to having index creation on.
finalizeAndWriteMetrics(LibraryIdGenerator, MetricsFile<DuplicationMetrics, Double>, File) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Writes the metrics given by the libraryIdGenerator to the outputFile.
finalizeMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Static method in class picard.illumina.ExtractBarcodesProgram
 
find(String, Class<?>) - Method in class picard.cmdline.ClassFinder
Scans the classpath for classes within the specified package and sub-packages that extend the parentType.
findAdapterPairAndIndexForSingleRead(byte[], int) - Method in class picard.util.AdapterMarker
Return the adapter to be trimmed from a read represented as an array of bytes[]
findAdapterPairAndIndexForSingleRead(byte[], int, double, int) - Method in class picard.util.AdapterMarker
Return the adapter to be trimmed from a read represented as an array of bytes[]
findAdapterPairAndIndexForSingleRead(byte[], int, double, int, AdapterPair...) - Static method in class picard.util.ClippingUtility
Return the adapter to be trimmed from a read represented as an array of bytes[]
findByKey(int) - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
 
findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
FindMendelianViolations - Class in picard.vcf.MendelianViolations
Summary
FindMendelianViolations() - Constructor for class picard.vcf.MendelianViolations.FindMendelianViolations
 
findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.
findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
Given a data type find the most preferred file format even if files are not available
findTile(int) - Method in class picard.illumina.parser.TileIndex
 
findTileMetricsFiles(File, int) - Static method in class picard.illumina.parser.TileMetricsUtil
Finds all of the tile metrics files for a given run directory and cycle count.
findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
Fingerprint - Class in picard.fingerprint
class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
Fingerprint(String, Path, String) - Constructor for class picard.fingerprint.Fingerprint
 
FINGERPRINT_DETAIL_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
 
FINGERPRINT_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
FINGERPRINT_GENOTYPES_VCF_FILE - Variable in class picard.arrays.GtcToVcf
 
FINGERPRINT_SUMMARY_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
 
FingerprintChecker - Class in picard.fingerprint
Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
FingerprintChecker(File) - Constructor for class picard.fingerprint.FingerprintChecker
Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.
FingerprintChecker(HaplotypeMap) - Constructor for class picard.fingerprint.FingerprintChecker
Creates a fingerprint checker that will work with the set of haplotyped provided.
fingerprintFiles(Collection<Path>, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads to speed up the processing.
FingerprintIdDetails - Class in picard.fingerprint
class to hold the details of a element of fingerprinting PU tag
FingerprintIdDetails() - Constructor for class picard.fingerprint.FingerprintIdDetails
 
FingerprintIdDetails(SAMReadGroupRecord, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
 
FingerprintIdDetails(String, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
 
FingerprintingDetailMetrics - Class in picard.analysis
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
FingerprintingDetailMetrics() - Constructor for class picard.analysis.FingerprintingDetailMetrics
 
FingerprintingSummaryMetrics - Class in picard.analysis
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
FingerprintingSummaryMetrics() - Constructor for class picard.analysis.FingerprintingSummaryMetrics
 
FingerprintMetrics - Class in picard.fingerprint
Class for holding metrics on a single fingerprint.
FingerprintMetrics() - Constructor for class picard.fingerprint.FingerprintMetrics
 
FingerprintResults - Class in picard.fingerprint
Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
FingerprintResults(Path, String, String) - Constructor for class picard.fingerprint.FingerprintResults
 
fingerprintSamFile(Path, IntervalList) - Method in class picard.fingerprint.FingerprintChecker
fingerprintSamFile(Path, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
Generates a Fingerprint per read group in the supplied SAM file using the loci provided in the interval list.
FingerprintUtils - Class in picard.fingerprint
A set of utilities used in the fingerprinting environment
FingerprintUtils() - Constructor for class picard.fingerprint.FingerprintUtils
 
FingerprintUtils.VariantContextSet - Class in picard.fingerprint
A class that holds VariantContexts sorted by genomic position
fingerprintVcf(Path) - Method in class picard.fingerprint.FingerprintChecker
 
finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
 
finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
 
finish() - Method in class picard.analysis.CollectGcBiasMetrics
 
finish() - Method in class picard.analysis.CollectInsertSizeMetrics
 
finish() - Method in class picard.analysis.CollectQualityYieldMetrics
 
finish() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
 
finish() - Method in class picard.analysis.CollectRnaSeqMetrics
 
finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
finish() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
 
finish() - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
finish() - Method in class picard.analysis.MeanQualityByCycle
 
finish() - Method in class picard.analysis.QualityScoreDistribution
 
finish() - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.
finish() - Method in class picard.metrics.MultiLevelCollector
Call finish on all PerUnitMetricCollectors
finish() - Method in interface picard.metrics.PerUnitMetricCollector
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
finish() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
FIRST - picard.illumina.parser.TileTemplateRead
 
FIRST - picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
 
FIRST_OF_PAIR - picard.analysis.AlignmentSummaryMetrics.Category
 
FIRST_READ_TRANSCRIPTION_STRAND - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
 
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
firstTile(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
Configures the first tile that the converter will begin processing at.
FisherStrandFilter - Class in picard.vcf.filter
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
 
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
 
FIVE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
FixedOffset - picard.util.BaitDesigner.DesignStrategy
Design that places baits at fixed offsets over targets, allowing them to hang off the ends as dictated by the target size and offset.
fixGenotypes(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.LiftoverUtils
 
FixMateInformation - Class in picard.sam
Summary
FixMateInformation() - Constructor for class picard.sam.FixMateInformation
 
fixNmMdAndUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
Calculates and sets the NM, MD, and and UQ tags from the record and the reference
fixUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
Calculates and sets UQ tag from the record and the reference
FixVcfHeader - Class in picard.vcf
Tool for replacing or fixing up a VCF header.
FixVcfHeader() - Constructor for class picard.vcf.FixVcfHeader
 
FLAG_DUPLICATES - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
flip() - Method in class picard.fingerprint.Snp
Returns a new SNP object with the alleles swapped and MAF corrected.
floatToByteArray(float) - Static method in class picard.arrays.illumina.InfiniumDataFile
Utility method to convert a float to a byte array
FLOWCELL_BARCODE - Variable in class picard.fastq.BamToBfq
 
FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
flowCellTileStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies base into their read's tile which is parsed from the read-name.
FlowCellTileStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
 
flowCellXStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies base into their read's tile which is parsed from the read-name.
FlowCellXStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
 
flowCellYStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies base into their read's tile which is parsed from the read-name.
FlowCellYStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
 
FLUIDIGM - picard.util.IlluminaUtil.IlluminaAdapterPair
 
FN - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The FN (false negative) count across all variants
FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.PanelMetricsBase
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
FOLD_80_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
The fold over-coverage necessary to raise 80% of bases to the mean coverage level.
FOLD_90_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
The fold over-coverage necessary to raise 90% of bases to the mean coverage level.
FOLD_95_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
The fold over-coverage necessary to raise 95% of bases to the mean coverage level.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
The fold by which the baited region has been amplified above genomic background.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fold by which the amplicon region has been amplified above genomic background.
FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetMetrics
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
foldInto(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics>) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
 
foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
formatFloatForVcf(float) - Static method in class picard.arrays.GtcToVcf
 
formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
A Map of file formats to the dataTypes they will provide for this run.
forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
Deprecated.
 
forVcf(PicardHtsPath) - Method in class picard.vcf.processor.VcfPathSegmentGenerator
 
FOUND_NO_EVIDENCE - picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
FP - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The FP (false positive) count across all variants
FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as reported for the fingerprinted sample
FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
 
FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of fragments in the SAM file
FREE - picard.illumina.DistanceMetric
 
freeDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
+++lifted from Commons Lang Text +++
fromBases(byte[]) - Static method in enum picard.fingerprint.DiploidGenotype
Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromBases(byte, byte) - Static method in enum picard.fingerprint.DiploidGenotype
Converts a pair of bases into a DiploidGenotype regardless of base order or case
fromCode(int) - Static method in enum picard.pedigree.Sex
Decodes the Sex from a numeric code.
fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
Attempts to read a pedigree file into memory.
fromPath(Path) - Static method in class picard.nio.PicardHtsPath
Construct a PicardHtsPath from a Path
fromPaths(Collection<String>) - Static method in class picard.nio.PicardHtsPath
Create a List from path representations.
fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
fromString(String) - Static method in enum picard.pedigree.Sex
Decodes the Sex from a String.
fullString() - Method in class picard.arrays.illumina.ArraysControlInfo
 
FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).

G

G - picard.analysis.artifacts.Transition.Base
 
G - picard.illumina.parser.IntensityChannel
 
G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of ref basecalls observed at sites where the genome reference == G.
GA4GH_CLIENT_SECRETS - Variable in class picard.cmdline.CommandLineProgram
 
GA4GHScheme - Class in picard.vcf
The scheme is defined in the constructor.
GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
 
GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
 
GatherBamFiles - Class in picard.sam
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
 
GatherVcfs - Class in picard.vcf
Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
 
GC - Variable in class picard.analysis.GcBiasDetailMetrics
The G+C content of the reference sequence represented by this bin.
GC_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
A measure of how undercovered >= 50% GC regions are relative to the mean.
GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
Illumina-style GC dropout metric.
GC_NC_0_19 - Variable in class picard.analysis.GcBiasSummaryMetrics
Normalized coverage over quintile of GC content ranging from 0 - 19.
GC_NC_20_39 - Variable in class picard.analysis.GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 20 - 39.
GC_NC_40_59 - Variable in class picard.analysis.GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 40 - 59.
GC_NC_60_79 - Variable in class picard.analysis.GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 60 - 79.
GC_NC_80_100 - Variable in class picard.analysis.GcBiasSummaryMetrics
Normalized coverage over each quintile of GC content ranging from 80 - 100.
GC_SCORE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
GcBiasDetailMetrics - Class in picard.analysis
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
 
GcBiasMetrics - Class in picard.metrics
 
GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
 
GcBiasMetricsCollector - Class in picard.analysis
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
 
GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
 
GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis
 
GcBiasSummaryMetrics - Class in picard.analysis
High level metrics that capture how biased the coverage in a certain lane is.
GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
 
GcBiasUtils - Class in picard.analysis
Utilities to calculate GC Bias Created by kbergin on 9/23/15.
GcBiasUtils() - Constructor for class picard.analysis.GcBiasUtils
 
gcContentStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
A stratifier that uses GC (of the read) to stratify.
GCContentStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
 
GCS - picard.nio.PathProvider
 
gencallVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
GENDER_CONCORDANCE_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether or not the three sexs agree
GENDER_GTC - Variable in class picard.arrays.GtcToVcf
 
Gene - Class in picard.annotation
Holds annotation of a gene for storage in an OverlapDetector.
Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
 
GENE_NAME - picard.annotation.RefFlatReader.RefFlatColumns
 
Gene.Transcript - Class in picard.annotation
A single transcript of a gene.
Gene.Transcript.Exon - Class in picard.annotation
1-based, inclusive representation of an exon.
GeneAnnotationReader - Class in picard.annotation
Load gene annotations into an OverlapDetector of Gene objects.
GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
 
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastq
 
generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastqWithTags
 
generateNoMatchBarcode(ReadStructure) - Static method in class picard.illumina.BarcodeExtractor
 
generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
 
generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
 
generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
Generates a read name string for the provided cluster.
generateShortName(ClusterData) - Method in class picard.fastq.Casava18ReadNameEncoder
 
generateShortName(ClusterData) - Method in class picard.fastq.IlluminaReadNameEncoder
 
generateShortName(ClusterData) - Method in interface picard.fastq.ReadNameEncoder
Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectRawWgsMetrics
 
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetrics
 
generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
 
GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
 
GENOME_BUILD_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
GENOME_SIZE - Variable in class picard.analysis.directed.PanelMetricsBase
The number of bases in the reference genome used for alignment.
GENOME_TERRITORY - Variable in class picard.analysis.WgsMetrics
The number of non-N bases in the genome reference over which coverage will be evaluated.
genotype - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The genotype concordance for all possible states.
GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CheckFingerprint
 
GenotypeConcordance - Class in picard.vcf
Summary
GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
 
GenotypeConcordance.Alleles - Class in picard.vcf
A simple structure to return the results of getAlleles.
GenotypeConcordanceContingencyMetrics - Class in picard.vcf
Class that holds metrics about the Genotype Concordance contingency tables.
GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
Empty constructor - needed for unit tests
GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
 
GenotypeConcordanceCounts - Class in picard.vcf
A class to store the counts for various truth and call state classifications relative to a reference.
GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
 
GenotypeConcordanceDetailMetrics - Class in picard.vcf
Class that holds detail metrics about Genotype Concordance
GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
 
GenotypeConcordanceScheme - Class in picard.vcf
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
 
GenotypeConcordanceSchemeFactory - Class in picard.vcf
Created by kbergin on 6/19/15.
GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
 
GenotypeConcordanceStateCodes - Enum in picard.vcf
Created by kbergin on 7/30/15.
GenotypeConcordanceStates - Class in picard.vcf
A class to store the various classifications for: 1.
GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
 
GenotypeConcordanceStates.CallState - Enum in picard.vcf
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
GenotypeConcordanceStates.ContingencyState - Enum in picard.vcf
A specific state for a 2x2 contingency table.
GenotypeConcordanceStates.TruthAndCallStates - Class in picard.vcf
A minute class to store the truth and call state respectively.
GenotypeConcordanceStates.TruthState - Enum in picard.vcf
These states represent the relationship between a truth genotype and the reference sequence.
GenotypeConcordanceSummaryMetrics - Class in picard.vcf
Class that holds summary metrics about Genotype Concordance
GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
Empty constructor - needed for unit tests
GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
 
GenotypeFilter - Interface in picard.vcf.filter
An interface for classes that perform Genotype filtration.
GenotypeQualityFilter - Class in picard.vcf.filter
Genotype filter that filters out genotypes below a given quality threshold.
GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
 
GENOTYPES - Variable in class picard.fingerprint.CheckFingerprint
 
genotypeScore - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
GENOTYPING_ERROR_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
 
GenotypingArraysProgramGroup - Class in picard.cmdline.programgroups
Miscellaneous tools, e.g.
GenotypingArraysProgramGroup() - Constructor for class picard.cmdline.programgroups.GenotypingArraysProgramGroup
 
get(int) - Method in class picard.analysis.CounterManager.Counter
 
get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
 
get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
 
get3PrimeAdapter() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
 
get3PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get3PrimeSoftClippedBases(Cigar, boolean) - Static method in class picard.analysis.AlignmentSummaryMetricsCollector
returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.
get5PrimeAdapter() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapter() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterBytes() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterBytesInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
 
get5PrimeAdapterInReadOrder() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
getAaCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getAbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
getAddressA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getAddressAId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getAddressB() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getAddressBId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getAlignedReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
getAllele1() - Method in enum picard.fingerprint.DiploidGenotype
 
getAllele1() - Method in class picard.fingerprint.Snp
 
getAllele2() - Method in enum picard.fingerprint.DiploidGenotype
 
getAllele2() - Method in class picard.fingerprint.Snp
 
getAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getAlleles() - Method in class picard.fingerprint.Snp
 
getAlleleString() - Method in class picard.fingerprint.Snp
 
getAllNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
 
getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
 
getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
Get the PerUnitMetricCollector that collects reads for all levels
getAllSnps() - Method in class picard.fingerprint.HaplotypeMap
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
getAllTiles() - Method in class picard.illumina.parser.readers.CbclReader
 
getAssayFormat() - Method in class picard.arrays.illumina.IlluminaManifest
 
getAssayHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
 
getAssayHeaderNameToIndex() - Method in class picard.arrays.illumina.IlluminaManifest
 
getAssayType() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getAttributesToReverse() - Method in class picard.sam.AbstractAlignmentMerger
Gets the set of attributes to be reversed on reads marked as negative strand.
getAttributesToReverseComplement() - Method in class picard.sam.AbstractAlignmentMerger
Gets the set of attributes to be reverse complemented on reads marked as negative strand.
getAutoCallDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getAutoCallVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Return the list of tiles available for this flowcell and lane.
getB37Chr() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getB37Pos() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getbAlleleFreqs() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getBarcode() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
 
getBarcodeValue(SAMRecord) - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
 
getBaseCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getBaseQualityHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
 
getBases() - Method in class picard.illumina.parser.BclData
 
getBases() - Method in class picard.illumina.parser.ReadData
 
getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetrics
If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
getBbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
 
getBeadSetId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
Returns the number of bytes that are in the buffer at the time of the method invocation.
getCallRate() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getCapacity() - Method in class picard.util.CircularByteBuffer
Returns the total capacity of the buffer (empty+filled).
getCategory() - Method in class picard.arrays.illumina.ArraysControlInfo
 
getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
We have to re-chain the program groups based on this algorithm.
getChr() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getChrom() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getChrom() - Method in class picard.fingerprint.Snp
 
getChromosomes() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
 
getClasses() - Method in class picard.cmdline.ClassFinder
Fetches the set of classes discovered so far.
getClusterCount() - Method in class picard.illumina.parser.Tile
Returns the number of on this tile.
getClusterDensity() - Method in class picard.illumina.parser.Tile
Returns the cluster density of this tile, in units of [cluster/mm^2].
getClusterFile() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.CallState
 
getCode() - Method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetrics
Creates AbstractWgsMetricsCollector implementation according to CollectWgsMetrics.USE_FAST_ALGORITHM value.
getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
getCommandLine() - Method in class picard.cmdline.CommandLineProgram
 
getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
 
getCommandLineParserForArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
 
getCompressedBlockSize() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
 
getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the concordance state array associate with the given truth state and call state tuple.
getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the contingency state array as a set
getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
Get the contingency state array as a parse-able string
getControl() - Method in class picard.arrays.illumina.ArraysControlInfo
 
getControlConfig() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the count defined by the truth state set and call state set.
getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
 
getCoverageByTarget() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Returns the accumulated coverage per target.
getCurrentLine() - Method in class picard.util.BasicInputParser
Provides access to the current (just parsed) line in pre-parsed format.
getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getCurrentLineNumber() - Method in class picard.util.BasicInputParser
NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
 
getCustomerStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getCycleData() - Method in class picard.illumina.parser.readers.CbclReader
 
getCycleFromDir(File) - Static method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
 
getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getDataTypesFromReadStructure(ReadStructure, boolean, File) - Static method in class picard.illumina.BasecallsConverter
Given a read structure return the data types that need to be parsed for this run
getDateFromVcfOtherHeaderLine(VCFHeader, String, SimpleDateFormat) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getDateManufactured() - Method in class picard.arrays.illumina.IlluminaManifest
 
getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
 
getDefaultSampleID() - Method in class picard.fingerprint.FingerprintChecker
 
getDensity() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
getDepthHistogram() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
 
getDepthHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
 
getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Gets the coverage depths as an array of ints.
getDescription() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.OtherProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.Testing
 
getDescription() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
 
getDescription() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
 
getDescriptorFileName() - Method in class picard.arrays.illumina.IlluminaManifest
 
getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getDictionaryForMergedBam() - Method in class picard.sam.AbstractAlignmentMerger
 
getDictionaryForMergedBam() - Method in class picard.sam.SamAlignmentMerger
 
getDiploidHaplotype(Snp, DiploidGenotype) - Method in class picard.fingerprint.HaplotypeBlock
Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
getDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getDuplicateMarkingsDiffer() - Method in class picard.sam.util.SamComparison
 
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
 
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
getDx() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getException() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
 
getExpClusters() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getExpClusters() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
getExtendedManifestVersion() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
 
getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
getExtension() - Static method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
 
getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
 
getFaqLink() - Static method in class picard.cmdline.CommandLineProgram
 
getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getFile() - Method in class picard.illumina.parser.TileIndex
 
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
 
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
 
getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
 
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
getFileName() - Method in class picard.util.AbstractInputParser
 
getFileName() - Method in class picard.util.BasicInputParser
Gets the name of the file being parsed
getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
 
getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
 
getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
getFilesForCycle(int) - Method in class picard.illumina.parser.readers.CbclReader
 
getFilteredBases() - Method in class picard.filter.CountingFilter
Gets the number of bases that have been filtered out thus far.
getFilteredRecords() - Method in class picard.filter.CountingFilter
Gets the number of records that have been filtered out thus far.
getFingerprintFile() - Method in class picard.fingerprint.MatchResults
 
getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType) - Static method in class picard.fingerprint.Fingerprint
 
getFingerprintMetrics(Fingerprint) - Method in class picard.fingerprint.CalculateFingerprintMetrics
 
getFingerprintPanels() - Method in class picard.fingerprint.Snp
 
getFirstSnp() - Method in class picard.fingerprint.HaplotypeBlock
Gets the arbitrarily first SNP in the haplotype.
getFlag() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getForceSort() - Method in class picard.sam.SamAlignmentMerger
 
getFracA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getFracC() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getFracG() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getFracT() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getFractionUnexpectedAlleleObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
getGender() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getGene() - Method in class picard.annotation.Gene.Transcript
 
getGenesForPickTranscripts() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
Derived class may override this method in order to return a different set of genes for picking transcripts for computing coverage, or to cache the value returned by geneOverlapDetector.getAll(), because it can be expensive to compute repeatedly.
getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getGenotype(String, InfiniumGTCRecord, IlluminaManifestRecord, Allele, Allele) - Method in class picard.arrays.GtcToVcf
 
getGenotypeBytes() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getGenotypeScores() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getGreen() - Method in class picard.arrays.illumina.ArraysControlInfo
 
getGroupMap(DocWorkUnit) - Method in class picard.util.help.PicardHelpDoclet
Adds a super-category so that we can custom-order the categories in the doc index
getHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the haplotype for which the probabilities apply.
getHaplotype(String) - Method in class picard.fingerprint.HaplotypeMap
Queries a HaplotypeBlock by Snp name.
getHaplotype(String, int) - Method in class picard.fingerprint.HaplotypeMap
Queries a HaplotypeBlock by Snp chromosome and position.
getHaplotype(Snp) - Method in class picard.fingerprint.HaplotypeMap
Queries a HaplotypeBlock by Snp object.
getHaplotypeFrequencies() - Method in class picard.fingerprint.HaplotypeBlock
Gets the set of haplotype frequencies.
getHaplotypeFrequency(int) - Method in class picard.fingerprint.HaplotypeBlock
Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
getHaplotypes() - Method in class picard.fingerprint.HaplotypeMap
Returns an unmodifiable collection of all the haplotype blocks in the map.
getHeader() - Method in class picard.fingerprint.FingerprintChecker
 
getHeader() - Method in class picard.fingerprint.HaplotypeMap
 
getHeader() - Method in class picard.sam.AbstractAlignmentMerger
 
getHeaderContents() - Method in class picard.arrays.illumina.IlluminaManifest
 
getHeaderSize() - Method in class picard.illumina.parser.readers.CbclReader
 
getHelpDoc() - Method in enum picard.analysis.CollectMultipleMetrics.Program
 
getHelpDoc() - Method in enum picard.illumina.DistanceMetric
 
getHelpDoc() - Method in enum picard.sam.FilterSamReads.Filter
 
getHelpDoc() - Method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
 
getHelpDoc() - Method in enum picard.sam.RevertSam.FileType
 
getHelpDoc() - Method in enum picard.util.IntervalList.IntervalListScatterMode
 
getHelpDoc() - Method in enum picard.util.IntervalListTools.Action
 
getHet(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
 
getHeterogyzousGenotype() - Method in class picard.fingerprint.Snp
 
getHetPercent() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getHgGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getHighQualityDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
 
getHistogram(long[], String, String) - Method in class picard.analysis.AbstractWgsMetricsCollector
 
getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
 
getHom(int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getHomozygousAllele1Genotype() - Method in class picard.fingerprint.Snp
 
getHomozygousAllele2Genotype() - Method in class picard.fingerprint.Snp
 
getIdentifier() - Method in class picard.arrays.illumina.InfiniumDataFile
 
getIlmnId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getIlmnId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getImagingDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getImagingUser() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
 
getIndelElement(SamLocusIterator.RecordAndOffset) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
 
getIndex() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getIndex() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getIndexTemplateName() - Method in class picard.util.help.PicardHelpDoclet
Return the name of the freemarker template to be used for the index generated by Barclay.
getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
 
getInfo() - Method in class picard.fingerprint.Fingerprint
 
getInputFile() - Method in class picard.fingerprint.FingerprintResults
 
getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
getInputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
 
getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
 
getIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getIntensityOnly() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getIntervalFile() - Method in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
 
getIntervalFile() - Method in interface picard.cmdline.argumentcollections.IntervalArgumentCollection
 
getIntervalList() - Method in class picard.fingerprint.HaplotypeMap
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
getIntervalsToExamine() - Method in class picard.analysis.CollectWgsMetrics
Gets the intervals over which we will calculate metrics.
getLane() - Method in class picard.illumina.parser.ClusterData
 
getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
Return the lane we're inspecting
getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getLaneFactories() - Method in class picard.illumina.BasecallsConverter
Gets the data provider factory used to create the underlying data provider.
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getLaneNumber() - Method in class picard.illumina.parser.Tile
Returns the number of this tile's parent lane.
getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getLastThreeFields(String, char, int[]) - Static method in class picard.sam.util.ReadNameParser
Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
getLeft() - Method in class picard.sam.util.Pair
 
getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getLibraryId() - Method in interface picard.sam.util.PhysicalLocation
 
getLibraryId() - Method in class picard.sam.util.PhysicalLocationInt
 
getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
Get the library ID for the given SAM record.
getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
Gets the library name from the header for the record.
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
 
getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
getLine() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getLine() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getLociCount() - Method in class picard.arrays.illumina.IlluminaManifest
 
getLociToGenotype(Collection<Fingerprint>) - Method in class picard.fingerprint.FingerprintChecker
Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.
getLocusEntries() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetrics
Creates AbstractLocusIterator implementation according to CollectWgsMetrics.USE_FAST_ALGORITHM value.
getLocusMaxReads() - Method in class picard.fingerprint.FingerprintChecker
 
getLocusResults() - Method in class picard.fingerprint.MatchResults
 
getLOD() - Method in class picard.fingerprint.MatchResults
 
getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the LOD score between the most probable haplotype and the second most probable.
getLodNT() - Method in class picard.fingerprint.MatchResults
 
getLodTN() - Method in class picard.fingerprint.MatchResults
 
getLog_of_base() - Method in class picard.util.MathUtil.LogMath
 
getLogFromProbability(double[]) - Static method in class picard.util.MathUtil
Takes a complete set of mutually exclusive Likelihoods and converts them to logLikelihoods.
getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
 
getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
getLogRDev() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getLogRRatios() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getLogValue(double) - Method in class picard.util.MathUtil.LogMath
Returns the log-representation of the provided decimal value.
getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
Returns the log-representation of the provided decimal array.
getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
getMaf() - Method in class picard.fingerprint.HaplotypeBlock
Returns the minor allele frequency of this haplotype.
getMaf() - Method in class picard.fingerprint.Snp
 
getMajorGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getManifestFile() - Method in class picard.arrays.illumina.IlluminaManifest
 
getManifestFileHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
 
getManifestFileParser() - Method in class picard.arrays.illumina.IlluminaManifest
 
getManifestName() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
getManifestName() - Method in class picard.arrays.illumina.InfiniumEGTFile
 
getMapInfo() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getMappingsDiffer() - Method in class picard.sam.util.SamComparison
 
getMappingsMatch() - Method in class picard.sam.util.SamComparison
 
getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
Returns the total of soft or hard masked bases in the interval of bases.
getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
 
getMatchResults() - Method in class picard.fingerprint.FingerprintResults
 
getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
 
getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
 
getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
 
getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
 
getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
 
getMessage(int) - Method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
 
getMetric() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
Returns the metric generated by the observed loci
getMetric() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
Returns the metric generated by the observed loci
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getMetrics() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
getMetrics() - Method in class picard.illumina.BarcodeExtractor
 
getMetrics() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
 
getMetrics() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
 
getMetrics(CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getMetricsCode() - Method in enum picard.illumina.parser.IlluminaMetricsCode
 
getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
Gets a MetricsFile with default headers already written into it.
getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getMinimumBaseQuality() - Method in class picard.illumina.BarcodeExtractor
 
getMinPairMatchBases() - Method in class picard.util.AdapterMarker
 
getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
 
getMismatches() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
 
getMismatchesToSecondBest() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
 
getMissingLeft() - Method in class picard.sam.util.SamComparison
 
getMissingRight() - Method in class picard.sam.util.SamComparison
 
getMostLikelyGenotype(Snp) - Method in class picard.fingerprint.HaplotypeProbabilities
Gets the genotype for this Snp given the most likely haplotype.
getMostLikelyHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
Gets the most likely haplotype given the probabilities.
getName() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getName() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getName() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.OtherProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.Testing
 
getName() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
 
getName() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
 
getName() - Method in class picard.fingerprint.Snp
 
getName() - Method in interface picard.util.AdapterPair
 
getName() - Method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
 
getNearProbeDistance() - Method in class picard.analysis.directed.TargetMetricsCollector
Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
getNextReadPair(PeekableIterator<SAMRecord>) - Static method in class picard.util.QuerySortedReadPairIteratorUtil
Get the next read pair (where both have the same read name).
getNodes() - Method in class picard.util.GraphUtils.Graph
 
getNoMatchMetric() - Method in class picard.illumina.BarcodeExtractor
 
getNoMatchMetric() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
 
getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
Returns the decimal representation of the provided log values.
getNonOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getNormalizationId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getNormalizedXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNormalizedYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
 
getNumAlignedBases(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
getNumAssays() - Method in class picard.arrays.illumina.IlluminaManifest
 
getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) - Static method in class picard.analysis.directed.TargetMetricsCollector
Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
 
getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getNumberOfSnps() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNumCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
 
getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
 
getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the number of duplicates detected
getNumIntensityOnly() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNumNoCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getNumReads() - Method in class picard.illumina.parser.ClusterData
 
getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Useful for statistics after the iterator has been exhausted and closed.
getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
 
getNumTiles() - Method in class picard.illumina.parser.TileIndex
 
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the number of observations of alleles supporting the first/major haplotype allele.
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
Returns the number of bases/reads that support the first allele.
getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the number of observations of alleles supporting the second/minor haplotype allele.
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
Returns the number of bases/reads that support the second allele.
getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
getOffset() - Method in class picard.arrays.illumina.InfiniumFileTOC
 
getOffsetX() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getOffsetY() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
getOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getOptionalDoubleFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getOptionalIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getOptionalValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
Returns a single byte that encodes the orientation of the two reads in a pair.
getOutputArgumentCollection() - Method in class picard.analysis.SinglePassSamProgram
 
getOutputArgumentCollection() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
 
getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
 
getOutputFile() - Method in class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
 
getOutputFile() - Method in interface picard.cmdline.argumentcollections.OutputArgumentCollection
 
getOutputFile() - Method in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
 
getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
 
getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
 
getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
getOutputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
getP05Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP05Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP10GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP50GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP50Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP50Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP95Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getP95Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getPackageList() - Static method in class picard.cmdline.PicardCommandLine
The packages we wish to include in our command line
getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
 
getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
getPGRecord(SAMFileHeader) - Method in class picard.cmdline.CommandLineProgram
 
getPhasingCode(int, IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Phasing codes are between 200 and 299 (inclusive).
getPhasingMap() - Method in class picard.illumina.parser.Tile
 
getPhasingMetricsForTiles(long, Collection<Tile>, boolean) - Static method in class picard.illumina.IlluminaPhasingMetrics
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
 
getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
 
getPlatformUnit() - Method in class picard.fingerprint.FingerprintIdDetails
 
getPloidy() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getPloidy() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getPloidy() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getPloidyType() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getPmtGreen() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getPmtRed() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
getPopulationLikelihood() - Method in class picard.fingerprint.MatchResults
 
getPos() - Method in class picard.fingerprint.Snp
 
getPosition() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getPositionInfo() - Method in class picard.illumina.parser.CbclData
 
getPositions() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
 
getPosteriorLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
getPrePhasingMap() - Method in class picard.illumina.parser.Tile
 
getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
 
getPrintableId() - Method in class picard.fingerprint.Fingerprint
 
getPriorProbablities() - Method in class picard.fingerprint.HaplotypeProbabilities
 
getProbabilityFromLog(double[]) - Static method in class picard.util.MathUtil
Takes a complete set of mutually exclusive logLikelihoods and converts them to probabilities with no rescaling.
getProbeIntervals() - Method in class picard.analysis.directed.CollectHsMetrics
 
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CollectHsMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
 
getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
 
getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
 
getQualities() - Method in class picard.illumina.parser.BclData
 
getQualities() - Method in class picard.illumina.parser.ReadData
 
getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
 
getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
getRawControlXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRawControlXIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRawControlYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRawControlYIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRawXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRawYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRead(int) - Method in class picard.illumina.parser.ClusterData
 
getReadBarcodeValue(SAMRecord, String) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
 
getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Gets the set of read ends
getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
Gets the read ends for optical duplicate tracking
getReadGroup() - Method in class picard.fingerprint.FingerprintResults
 
getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
 
getReadGroup() - Method in interface picard.sam.util.PhysicalLocation
 
getReadGroup() - Method in class picard.sam.util.PhysicalLocationInt
 
getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
 
getReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
getReadType() - Method in class picard.illumina.parser.ReadData
 
getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getRecord(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
getRed() - Method in class picard.arrays.illumina.ArraysControlInfo
 
getRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getReferenceFasta() - Method in class picard.fingerprint.FingerprintChecker
 
getReferenceFile() - Method in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
 
getReferenceFile() - Method in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
 
getReferenceFile() - Method in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
 
getReferenceFile() - Method in interface picard.cmdline.argumentcollections.ReferenceArgumentCollection
 
getReferenceFile() - Method in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
 
getReferenceFile() - Method in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
 
getReferenceFile() - Method in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
 
getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
 
getReferenceStrand() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getRefStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getRefStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns a representative SNP for this haplotype.
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
Returns the SNP who's genotype was used to construct the likelihoods.
getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
getReserved1() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getReserved2() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getReserved3() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getReserved4() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getReserved5() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getReserved6() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getRight() - Method in class picard.sam.util.Pair
 
getRIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getRsId() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getRunFile(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
 
getSamFileHeader() - Method in class picard.analysis.CollectWgsMetrics
This method should only be called after CollectWgsMetrics.getSamReader() is called.
getSample() - Method in class picard.fingerprint.Fingerprint
 
getSample() - Method in class picard.fingerprint.FingerprintIdDetails
 
getSample() - Method in class picard.fingerprint.MatchResults
 
getSampleAlias() - Method in class picard.fingerprint.FingerprintResults
 
getSampleLikelihood() - Method in class picard.fingerprint.MatchResults
 
getSampleName() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getSamplePlate() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getSampleWell() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getSamReader() - Method in class picard.analysis.CollectWgsMetrics
Gets the SamReader from which records will be examined.
getSamReader() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
 
getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
 
getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
A number of convenience functions
getScaleX() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getScaleY() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getScannerName() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getScannerVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
 
getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sensitivity defined by the scheme across the subset of truth states.
getSentrixBarcode() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getSequentialFileList(File) - Static method in class picard.sam.FastqToSam
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
getSex() - Method in class picard.pedigree.PedFile.PedTrio
 
getSexConcordance(String, String, String) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics
 
getShear() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getSingleBarcodeDistanceQuery(int, int) - Method in class picard.util.BarcodeEditDistanceQuery
 
getSingletonSample(VariantContext) - Static method in class picard.vcf.CallingMetricAccumulator
 
getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
getSnp() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSnp(String) - Method in class picard.fingerprint.HaplotypeBlock
Gets a SNP by name if it belongs to this haplotype.
getSnp(String, int) - Method in class picard.fingerprint.HaplotypeMap
Queries a Snp by chromosome and position.
getSnpAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getSnpAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
 
getSnpGenotype(Snp, DiploidHaplotype) - Method in class picard.fingerprint.HaplotypeBlock
Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
getSnpManifest() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getSnpRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
getSnps() - Method in class picard.fingerprint.HaplotypeBlock
Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
getSource() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSource() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSource() - Method in class picard.fingerprint.Fingerprint
 
getSourceSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSourceSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSourceStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSourceStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSourceVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSourceVersion() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSpecies() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getSpecies() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the specificity defined by the scheme across the subset of truth states.
getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
 
getStandardUsagePreamble(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
A typical command line program will call this to get the beginning of the usage message, and then typically append a description of the program, like this: public String USAGE = getStandardUsagePreamble(getClass()) + "Frobnicate the freebozle."
getSuffix() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
 
getSuffix() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
The suffix that pertains to the implementation of aggregation
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
 
getSuffix() - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
 
getSuffix() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
The suffix that pertains to the implementation of aggregation
getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
getSuperCategoryMap() - Static method in class picard.util.help.HelpConstants
 
getSuperCategoryProperty(String) - Static method in class picard.util.help.HelpConstants
Given a group name, return a supercategory string for use by the online doc system to determine which supercateogry the group is in.
getTagFilterPrefix() - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
 
getTemplateName(DocWorkUnit) - Method in class picard.util.help.PicardHelpDocWorkUnitHandler
 
getTheta() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getThetaIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
 
getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
 
getTile() - Method in class picard.illumina.parser.CbclData
 
getTile() - Method in class picard.illumina.parser.ClusterData
 
getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
getTile() - Method in interface picard.sam.util.PhysicalLocation
 
getTile() - Method in class picard.sam.util.PhysicalLocationInt
 
getTiledFiles(File, Pattern) - Static method in class picard.illumina.BasecallsConverter
Applies an lane and tile based regex to return all files matching that regex for each tile.
getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
Return all files that match pattern of the given file type in the given base directory
getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
Parse the tile # from the read name.
getTileInfo() - Method in class picard.illumina.parser.readers.BaseBclReader.CycleData
 
getTileNum() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
 
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
getTileNumber() - Method in class picard.illumina.parser.Tile
Returns the number/name of this tile.
getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
 
getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
 
getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
Return a list of all tiles available for this file format and run
getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
getTiles() - Method in class picard.illumina.parser.TileIndex
 
getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
 
getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
 
getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns the total number of observations of any allele.
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
Gets the total number of observations presented at this locus.
getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
 
getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
getUnfilteredBaseQHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
 
getUnfilteredDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
 
getUniqueNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
 
getUnmappedBoth() - Method in class picard.sam.util.SamComparison
 
getUnmappedLeft() - Method in class picard.sam.util.SamComparison
 
getUnmappedRight() - Method in class picard.sam.util.SamComparison
 
getUnsupportedBuilds() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
Given a file type, get the Parameterized File Util object associated with it
getValidationStringency() - Method in class picard.fingerprint.FingerprintChecker
 
getValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
 
getVar(int, int) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
 
getVariantTypeFromOrdinal(int) - Static method in enum picard.util.VariantType
Gets the enum for a given ordinal
getVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
getVersion() - Method in class picard.arrays.illumina.InfiniumTransformation
 
getVersion() - Method in class picard.cmdline.CommandLineProgram
 
getVersion() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
getWordCount() - Method in class picard.util.AbstractInputParser
 
getX() - Method in class picard.illumina.parser.ClusterData
 
getX() - Method in interface picard.sam.util.PhysicalLocation
 
getX() - Method in class picard.sam.util.PhysicalLocationInt
 
getXCoordinate() - Method in class picard.illumina.parser.CbclData
 
getY() - Method in class picard.illumina.parser.ClusterData
 
getY() - Method in interface picard.sam.util.PhysicalLocation
 
getY() - Method in class picard.sam.util.PhysicalLocationInt
 
getYCoordinate() - Method in class picard.illumina.parser.CbclData
 
getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
 
GG - picard.fingerprint.DiploidGenotype
 
Graph() - Constructor for class picard.util.GraphUtils.Graph
 
GraphUtils - Class in picard.util
Created by farjoun on 11/2/16.
GraphUtils() - Constructor for class picard.util.GraphUtils
 
GraphUtils.Graph<Node extends Comparable<Node>> - Class in picard.util
 
GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
The green intensity value for the control.
GroupAlignmentSummaryMetricsPerUnitMetricCollector(String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
 
GT - picard.fingerprint.DiploidGenotype
 
GT_FILTERED - picard.vcf.GenotypeConcordanceStates.CallState
 
GT_FILTERED - picard.vcf.GenotypeConcordanceStates.TruthState
 
GT_FILTERED_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
GTA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
GTC_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The call rate as determined by Autocall/IAAP (and stored in the GTC File)
GTC_CALL_RATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
GTC_CALL_RATE_DETAIL - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
GtcToVcf - Class in picard.arrays
Class to convert an Illumina GTC file into a VCF file.
GtcToVcf() - Constructor for class picard.arrays.GtcToVcf
 
GtoA - picard.analysis.artifacts.Transition
 
GtoC - picard.analysis.artifacts.Transition
 
GtoG - picard.analysis.artifacts.Transition
 
GtoT - picard.analysis.artifacts.Transition
 
GTZ - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
GVCF_INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
GvcfMetricAccumulator - Class in picard.vcf
An accumulator for collecting metrics about a single-sample GVCF.
GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.GvcfMetricAccumulator
 

H

HAMMING - picard.illumina.DistanceMetric
 
hammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
 
handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastq
 
handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastqWithTags
 
handleItem(String) - Method in class picard.cmdline.ClassFinder
Checks an item to see if it is a class and is annotated with the specified annotation.
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CheckFingerprint
 
HAPLOTYPE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
 
HAPLOTYPE_MAP - Variable in class picard.fingerprint.ExtractFingerprint
 
HAPLOTYPE_MAP - Variable in class picard.fingerprint.IdentifyContaminant
 
HaplotypeBlock - Class in picard.fingerprint
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
HaplotypeBlock(double) - Constructor for class picard.fingerprint.HaplotypeBlock
Constructs a haplotype block with the provided minor allele frequency.
HaplotypeMap - Class in picard.fingerprint
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
HaplotypeMap(SAMFileHeader) - Constructor for class picard.fingerprint.HaplotypeMap
Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
HaplotypeMap(File) - Constructor for class picard.fingerprint.HaplotypeMap
 
HaplotypeMap(Collection<HaplotypeBlock>) - Constructor for class picard.fingerprint.HaplotypeMap
since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!
HaplotypeProbabilities - Class in picard.fingerprint
Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
HaplotypeProbabilities(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilities
 
HaplotypeProbabilities.Genotype - Enum in picard.fingerprint
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
HaplotypeProbabilitiesFromContaminatorSequence - Class in picard.fingerprint
Represents the probability of the underlying haplotype of the contaminating sample given the data.
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
HaplotypeProbabilitiesFromGenotype - Class in picard.fingerprint
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
 
HaplotypeProbabilitiesFromGenotype(Snp, HaplotypeBlock, double, double, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
 
HaplotypeProbabilitiesFromGenotypeLikelihoods - Class in picard.fingerprint
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
 
HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
 
HaplotypeProbabilitiesFromSequence - Class in picard.fingerprint
Represents the probability of the underlying haplotype given the data.
HaplotypeProbabilitiesFromSequence(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
HaplotypeProbabilityOfNormalGivenTumor - Class in picard.fingerprint
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilityOfNormalGivenTumor) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
HAPLOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
Number of haplotypes examined
HAPLOTYPES_CONFIDENTLY_CHECKED - Variable in class picard.analysis.FingerprintingSummaryMetrics
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.
HAPLOTYPES_CONFIDENTLY_MATCHING - Variable in class picard.analysis.FingerprintingSummaryMetrics
The subset of confidently checked haplotypes that match the expected genotypes.
HAPLOTYPES_WITH_EVIDENCE - Variable in class picard.fingerprint.FingerprintMetrics
Number of haplotypes that had evidence in the source file
HAPLOTYPES_WITH_GENOTYPES - Variable in class picard.analysis.FingerprintingSummaryMetrics
The number of haplotypes that had expected genotypes to compare to.
HARD_CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
 
hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
True if this record has paternal and maternal ids, otherwise false.
hasCbcls(File, int) - Static method in class picard.illumina.parser.IlluminaFileUtil
 
hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
 
hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Returns true if any base in the range has coverage of > 0
hasError() - Method in class picard.util.ThreadPoolExecutorWithExceptions
 
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns true if evidence has been added, false if the probabilities are just the priors.
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
hashCode() - Method in class picard.annotation.Gene.Transcript
 
hashCode() - Method in class picard.fingerprint.FingerprintIdDetails
 
hashCode() - Method in class picard.fingerprint.HaplotypeBlock
 
hashCode() - Method in class picard.fingerprint.Snp
 
hashCode() - Method in class picard.illumina.parser.Range
 
hashCode() - Method in class picard.illumina.parser.ReadDescriptor
 
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
hashCode() - Method in class picard.illumina.parser.ReadStructure
 
hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
hashCode() - Method in class picard.sam.util.Pair
Basic hashcode function.
hashCode() - Method in class picard.sam.util.PrimaryAlignmentKey
 
hashCode() - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
hasLocation() - Method in interface picard.sam.util.PhysicalLocation
Default implementation of a method to check whether real location data has been set.
hasNext() - Method in class picard.illumina.parser.MultiTileParser
 
hasNext() - Method in class picard.illumina.parser.PerTileParser
 
hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Return true if the file has more elements to return, false otherwise
hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.BclReader
 
hasNext() - Method in class picard.illumina.parser.readers.CbclReader
 
hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
 
hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
 
hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
hasNext() - Method in class picard.util.AsyncIterator
 
hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
hasNext() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
hasNext() - Method in class picard.vcf.PairedVariantSubContextIterator
 
hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
hasSampleBarcode() - Method in class picard.illumina.parser.ReadStructure
 
hasWebDocumentation(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
Determine if a class has web documentation based on its package name
header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
HEADER - Variable in class picard.sam.ReplaceSamHeader
 
HEADER - Variable in class picard.vcf.FixVcfHeader
 
HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
 
HEADER_ONLY - Variable in class picard.sam.ViewSam
 
headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
 
headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
 
headerLines() - Method in class picard.vcf.filter.QdFilter
 
headerLines() - Method in interface picard.vcf.filter.VariantFilter
Return VCF header lines that define filters that may be applied by the VariantFilter.
HelpConstants - Class in picard.util.help
 
HET_ALLELE12 - picard.fingerprint.HaplotypeProbabilities.Genotype
 
HET_AS_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
num of hets, observed as homs with LOD > threshold
HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)
HET_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)
HET_GENOTYPE_FOR_PHASING - Static variable in class picard.fingerprint.HaplotypeMap
 
HET_HOMVAR_RATIO - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
(count of hets)/(count of homozygous non-ref) for this sample
HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
(count of hets)/(count of homozygous non-ref) for this sample
HET_PCT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
100 * (count of hets) / (total calls) for this sample
HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
HET_REF_VAR1 - picard.vcf.GenotypeConcordanceStates.CallState
 
HET_REF_VAR1 - picard.vcf.GenotypeConcordanceStates.TruthState
 
HET_REF_VAR1_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
HET_REF_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
 
HET_REF_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
 
HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
HET_SNP_Q - Variable in class picard.analysis.directed.PanelMetricsBase
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
HET_SNP_Q - Variable in class picard.analysis.WgsMetrics
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.PanelMetricsBase
The theoretical HET SNP sensitivity.
HET_SNP_SENSITIVITY - Variable in class picard.analysis.WgsMetrics
The theoretical HET SNP sensitivity.
HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all heterozygous variants cannot be calculated
HET_VAR1_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
 
HET_VAR1_VAR2 - picard.vcf.GenotypeConcordanceStates.TruthState
 
HET_VAR1_VAR2_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
HET_VAR1_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
 
HET_VAR3_VAR4 - picard.vcf.GenotypeConcordanceStates.CallState
 
hetAltDepthDistribution(int) - Static method in class picard.analysis.TheoreticalSensitivity
 
hetSNPSensitivity(double[], double[], int, double) - Static method in class picard.analysis.TheoreticalSensitivity
 
hetSNPSensitivity(double[], double[], int, double, boolean) - Static method in class picard.analysis.TheoreticalSensitivity
 
HG_TO_NCBI - Static variable in class picard.arrays.illumina.IlluminaManifest
 
HG17 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
HG18 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
HG19 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
highQualityDepthHistogram - Variable in class picard.analysis.WgsMetrics
Count of sites with a given depth of coverage.
highQualityDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
Count of sites with a given depth of coverage.
Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
 
HISTOGRAM_FILE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
Histogram_R_SCRIPT - Static variable in class picard.analysis.CollectInsertSizeMetrics
 
HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
 
HOM_ALLELE1 - picard.fingerprint.HaplotypeProbabilities.Genotype
 
HOM_ALLELE2 - picard.fingerprint.HaplotypeProbabilities.Genotype
 
HOM_AS_HET - Variable in class picard.analysis.FingerprintingSummaryMetrics
num of homs, observed as hets with LOD > threshold
HOM_AS_OTHER_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
num of homs, observed as other homs with LOD > threshold
HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
The Chi-squared pvalue for FingerprintMetrics.NUM_HOM_ALLELE1 and FingerprintMetrics.NUM_HOM_ALLELE2 relative to the expected counts (2x2 table)
HOM_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
The categorical cross entropy of FingerprintMetrics.NUM_HOM_ALLELE1 and FingerprintMetrics.NUM_HOM_ALLELE2 relative to the expected counts (big is bad)
HOM_REF - picard.vcf.GenotypeConcordanceStates.CallState
 
HOM_REF - picard.vcf.GenotypeConcordanceStates.TruthState
 
HOM_REF_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
HOM_VAR1 - picard.vcf.GenotypeConcordanceStates.CallState
 
HOM_VAR1 - picard.vcf.GenotypeConcordanceStates.TruthState
 
HOM_VAR1_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
HOM_VAR2 - picard.vcf.GenotypeConcordanceStates.CallState
 
HOM_VAR3 - picard.vcf.GenotypeConcordanceStates.CallState
 
homoPolymerLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the length of the homopolymer preceding it (in the read direction).
homopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.
HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all homozygous variants cannot be calculated.
HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
The estimated number of unique molecules in the selected part of the library.
HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
HsMetricCollector - Class in picard.analysis.directed
Calculates HS metrics for a given SAM or BAM file.
HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
 
HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
 
HsMetrics - Class in picard.analysis.directed
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics
 

I

ID - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
The ID of this entry
identifyContaminant(Path, double) - Method in class picard.fingerprint.FingerprintChecker
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
IdentifyContaminant - Class in picard.fingerprint
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
IdentifyContaminant() - Constructor for class picard.fingerprint.IdentifyContaminant
 
IGC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
IGNORE - Variable in class picard.sam.ValidateSamFile
 
IGNORE_FILTER_STATUS - Variable in class picard.vcf.GenotypeConcordance
 
IGNORE_HISTOGRAM_DIFFERENCES - Variable in class picard.analysis.CompareMetrics
 
IGNORE_MISSING_MATES - Variable in class picard.sam.FixMateInformation
 
IGNORE_READ_GROUPS - Variable in class picard.fingerprint.CheckFingerprint
 
IGNORE_SEQUENCE - Variable in class picard.analysis.CollectMultipleMetrics
 
IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
 
IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToSam
 
IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
 
ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
For now, we ignore only those alignments that have more than SamAlignmentMerger.maxGaps insertions or deletions.
IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
ignoreUnexpectedBarcodes - Variable in class picard.illumina.BasecallsConverter
 
ILLUMINA - picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
 
ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
 
ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.GtcToVcf
 
ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.illumina.CompareGtcFiles
 
ILLUMINA_BUILD - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ILLUMINA_CHR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ILLUMINA_FLAGGED - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Flagged by Illumina as a bad assay
ILLUMINA_FLAGGED_BAD_CHR - Static variable in class picard.arrays.illumina.IlluminaManifestRecord
 
ILLUMINA_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
ILLUMINA_POS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ILLUMINA_STRAND - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ILLUMINA_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
IlluminaAdpcFileWriter - Class in picard.arrays.illumina
A class to encompass writing an Illumina adpc.bin file.
IlluminaAdpcFileWriter(File) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter
 
IlluminaAdpcFileWriter.Record - Class in picard.arrays.illumina
 
IlluminaBasecallingMetrics - Class in picard.illumina
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
 
IlluminaBasecallsToFastq - Class in picard.illumina
 
IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
 
IlluminaBasecallsToFastq.ReadNameFormat - Enum in picard.illumina
Simple switch to control the read name format to emit.
IlluminaBasecallsToSam - Class in picard.illumina
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
 
IlluminaBPMFile - Class in picard.arrays.illumina
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
IlluminaBPMFile(File) - Constructor for class picard.arrays.illumina.IlluminaBPMFile
 
IlluminaBPMLocusEntry - Class in picard.arrays.illumina
A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
IlluminaBPMLocusEntry() - Constructor for class picard.arrays.illumina.IlluminaBPMLocusEntry
 
IlluminaDataProviderFactory - Class in picard.illumina.parser
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
Create factory with the specified options, one that favors using QSeqs over all other files
IlluminaDataType - Enum in picard.illumina.parser
List of data types of interest when parsing Illumina data.
IlluminaFileUtil - Class in picard.illumina.parser
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
 
IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
 
IlluminaFileUtil.SupportedIlluminaFormat - Enum in picard.illumina.parser
 
IlluminaGenotype - Enum in picard.arrays.illumina
 
IlluminaLaneMetrics - Class in picard.illumina
Embodies characteristics that describe a lane.
IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
 
IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
 
IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
 
IlluminaManifest - Class in picard.arrays.illumina
A class to represent an Illumina Manifest file.
IlluminaManifest(File) - Constructor for class picard.arrays.illumina.IlluminaManifest
 
IlluminaManifest(File, int) - Constructor for class picard.arrays.illumina.IlluminaManifest
 
IlluminaManifestRecord - Class in picard.arrays.illumina
A class to represent a record (line) from an Illumina Manifest [Assay] entry
IlluminaManifestRecord.IlluminaStrand - Enum in picard.arrays.illumina
 
IlluminaMetricsCode - Enum in picard.illumina.parser
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
IlluminaPhasingMetrics - Class in picard.illumina
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
 
IlluminaReadNameEncoder - Class in picard.fastq
A read name encoder following the encoding initially produced by picard fastq writers.
IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
 
IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
IlluminaTileMetrics(ByteBuffer, TileMetricsOutReader.TileMetricsVersion) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
IlluminaUtil - Class in picard.util
Misc utilities for working with Illumina specific files and data
IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
 
IlluminaUtil.IlluminaAdapterPair - Enum in picard.util
Describes adapters used on each pair of strands
IMAGING_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The date that this sample was imaged
IMAGING_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
IMPROPER - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
in - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
in - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
INCLUDE_BARCODE_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
 
INCLUDE_BC_IN_RG_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
 
INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
 
INCLUDE_DUPLICATES - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INCLUDE_DUPLICATES - Variable in class picard.analysis.CollectInsertSizeMetrics
 
INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
 
INCLUDE_FILTERED - Variable in class picard.vcf.VcfToIntervalList
 
INCLUDE_FILTERED_SHORT_NAME - Static variable in class picard.vcf.VcfToIntervalList
 
INCLUDE_INDELS - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
 
INCLUDE_NON_PF_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INCLUDE_NON_PF_READS - Variable in class picard.analysis.CollectOxoGMetrics
 
INCLUDE_NON_PF_READS - Variable in class picard.fastq.BamToBfq
 
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
 
INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
 
INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
 
INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
 
INCLUDE_SUPPLEMENTAL_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
 
INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INCLUDE_UNPAIRED - Variable in class picard.analysis.CollectMultipleMetrics
 
includeAligned - picard.sam.FilterSamReads.Filter
 
includeJavascript - picard.sam.FilterSamReads.Filter
 
includeNonPfReads - Variable in class picard.illumina.BasecallsConverter
 
includePairedIntervals - picard.sam.FilterSamReads.Filter
 
includeReadList - picard.sam.FilterSamReads.Filter
 
includeSupplementalAlignments - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
 
includeTagValues - picard.sam.FilterSamReads.Filter
 
INCOMPARABLE_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
INCONCLUSIVE - picard.fingerprint.CrosscheckMetric.FingerprintResult
 
INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
Number of aligned reads that are mapped to the incorrect strand.
increment(int) - Method in class picard.analysis.CounterManager.Counter
Increments value corresponding to reference sequence index
increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
Increments a count for the truth/call state tuple.
increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
 
incrementReadCount() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
Increments the # of reads mapping to this target.
INDEL_CONFLICT - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Both insertion and deletion sequence found in reference.
INDEL_EXTENSION_ERROR - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
INDEL_NOT_FOUND - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Neither insertion nor deletion sequence found in reference.
INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
 
INDEL_SEQ_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
indelCounter - Variable in class picard.vcf.GenotypeConcordance
 
IndelErrorCalculator - Class in picard.sam.SamErrorMetric
A calculator that estimates the error rate of the bases it observes for indels only.
IndelErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.IndelErrorCalculator
 
IndelErrorMetric - Class in picard.sam.SamErrorMetric
Metric to be used for InDel errors
IndelErrorMetric() - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
 
IndelErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
 
indelLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the number of bases in an insertion
IndelLengthStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
 
indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
indelsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratify by Indels in the read cigars.
IndelsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
 
IndependentReplicateMetric - Class in picard.analysis.replicates
A class to store information relevant for biological rate estimation
IndependentReplicateMetric() - Constructor for class picard.analysis.replicates.IndependentReplicateMetric
 
independentReplicationRateFromBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
 
independentReplicationRateFromTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
independentReplicationRateFromUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets.
INDEX_VALIDATION_STRINGENCY - Variable in class picard.sam.ValidateSamFile
 
INDEXED - picard.util.IlluminaUtil.IlluminaAdapterPair
 
indexOfMax(double[]) - Static method in class picard.util.MathUtil
Returns the index of the largest element in the array.
indexOfMax(long[]) - Static method in class picard.util.MathUtil
Returns the index of the largest element in the array.
indexOfMin(double[]) - Static method in class picard.util.MathUtil
Returns the index of the smallest element in the array.
indexOfMin(int[]) - Static method in class picard.util.MathUtil
Returns the index of the smallest element in the array.
IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category, String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
 
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
Label the artifacts corresponding to known error modes.
inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
Label the artifacts corresponding to known error modes.
INFERRED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.
INFERRED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
Number of different inferred UMI sequences derived
InfiniumDataFile - Class in picard.arrays.illumina
A class to provide methods for accessing Illumina Infinium Data Files.
InfiniumEGTFile - Class in picard.arrays.illumina
A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
InfiniumEGTFile(File) - Constructor for class picard.arrays.illumina.InfiniumEGTFile
 
InfiniumFileTOC - Class in picard.arrays.illumina
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
InfiniumFileTOC() - Constructor for class picard.arrays.illumina.InfiniumFileTOC
 
InfiniumGTCFile - Class in picard.arrays.illumina
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
InfiniumGTCFile(File, File) - Constructor for class picard.arrays.illumina.InfiniumGTCFile
Creates an InfiniumGTCFile object and parses the given input file.
InfiniumGTCRecord - Class in picard.arrays.illumina
 
InfiniumGTCRecord(String) - Constructor for class picard.arrays.illumina.InfiniumGTCRecord
 
InfiniumNormalizationManifest - Class in picard.arrays.illumina
A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
InfiniumNormalizationManifest(File) - Constructor for class picard.arrays.illumina.InfiniumNormalizationManifest
 
InfiniumTransformation - Class in picard.arrays.illumina
 
InfiniumTransformation() - Constructor for class picard.arrays.illumina.InfiniumTransformation
 
InfiniumVcfFields - Class in picard.arrays.illumina
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
InfiniumVcfFields() - Constructor for class picard.arrays.illumina.InfiniumVcfFields
 
InfiniumVcfFields.GENOTYPE_VALUES - Enum in picard.arrays.illumina
 
INFO - Variable in class picard.fingerprint.FingerprintMetrics
Additional information about the fingerprint
initialize() - Method in class picard.illumina.parser.MultiTileBclParser
 
initialize() - Method in enum picard.nio.PathProvider
 
initializeAdditionalWriters() - Method in class picard.sam.SamToFastq
 
initializeAdditionalWriters() - Method in class picard.sam.SamToFastqWithTags
 
initiateScheme() - Method in class picard.vcf.GA4GHScheme
 
initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
 
initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
 
INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
INPUT - Variable in class picard.analysis.CollectMultipleMetrics
 
INPUT - Variable in class picard.analysis.CollectOxoGMetrics
 
INPUT - Variable in class picard.analysis.CollectRrbsMetrics
 
INPUT - Variable in class picard.analysis.CollectWgsMetrics
 
INPUT - Variable in class picard.analysis.CompareMetrics
 
INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
INPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
INPUT - Variable in class picard.analysis.SinglePassSamProgram
 
INPUT - Variable in class picard.annotation.SortGff
 
INPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
INPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
 
INPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
 
INPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
 
INPUT - Variable in class picard.arrays.GtcToVcf
 
INPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
 
INPUT - Variable in class picard.arrays.illumina.CompareGtcFiles
 
INPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
INPUT - Variable in class picard.fastq.BamToBfq
 
INPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
INPUT - Variable in class picard.fingerprint.CheckFingerprint
 
INPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
 
INPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
 
INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
 
INPUT - Variable in class picard.fingerprint.ExtractFingerprint
 
INPUT - Variable in class picard.fingerprint.IdentifyContaminant
 
INPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
 
INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
 
INPUT - Variable in class picard.reference.NonNFastaSize
 
INPUT - Variable in class picard.reference.NormalizeFasta
 
INPUT - Variable in class picard.sam.AddCommentsToBam
 
INPUT - Variable in class picard.sam.AddOATag
 
INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
 
INPUT - Variable in class picard.sam.BamIndexStats
 
INPUT - Variable in class picard.sam.BuildBamIndex
 
INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
 
INPUT - Variable in class picard.sam.CheckTerminatorBlock
 
INPUT - Variable in class picard.sam.CleanSam
 
INPUT - Variable in class picard.sam.DownsampleSam
 
INPUT - Variable in class picard.sam.FilterSamReads
 
INPUT - Variable in class picard.sam.FixMateInformation
 
INPUT - Variable in class picard.sam.GatherBamFiles
 
INPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
 
INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
INPUT - Variable in class picard.sam.MergeSamFiles
 
INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
 
INPUT - Variable in class picard.sam.ReorderSam
 
INPUT - Variable in class picard.sam.ReplaceSamHeader
 
INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
INPUT - Variable in class picard.sam.RevertSam
 
INPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
INPUT - Variable in class picard.sam.SamFormatConverter
 
INPUT - Variable in class picard.sam.SamToFastq
 
INPUT - Variable in class picard.sam.SetNmMdAndUqTags
 
INPUT - Variable in class picard.sam.SortSam
 
INPUT - Variable in class picard.sam.SplitSamByLibrary
 
INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
 
INPUT - Variable in class picard.sam.ValidateSamFile
 
INPUT - Variable in class picard.sam.ViewSam
 
INPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
 
INPUT - Variable in class picard.util.BedToIntervalList
 
INPUT - Variable in class picard.util.IntervalListToBed
 
INPUT - Variable in class picard.util.IntervalListTools
 
INPUT - Variable in class picard.util.LiftOverIntervalList
 
INPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
 
INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
INPUT - Variable in class picard.vcf.filter.FilterVcf
 
INPUT - Variable in class picard.vcf.FixVcfHeader
 
INPUT - Variable in class picard.vcf.GatherVcfs
 
INPUT - Variable in class picard.vcf.LiftoverVcf
 
INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
 
INPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
 
INPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
INPUT - Variable in class picard.vcf.MergeVcfs
 
INPUT - Variable in class picard.vcf.RenameSampleInVcf
 
INPUT - Variable in class picard.vcf.SortVcf
 
INPUT - Variable in class picard.vcf.SplitVcfs
 
INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
INPUT - Variable in class picard.vcf.VcfFormatConverter
 
INPUT - Variable in class picard.vcf.VcfToIntervalList
 
INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
INPUT_PARAMS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
 
INPUT_SAMPLE_FILE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
 
INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
 
INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
inputReadStructure - Variable in class picard.illumina.ExtractBarcodesProgram
The read structure of the actual Illumina Run, i.e.
insertion - picard.util.VariantType
 
INSERTIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The (phred) rate of insertions.
insertionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratify by Insertions in the read cigars.
insertLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
InsertSizeMetrics - Class in picard.analysis
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
 
InsertSizeMetricsCollector - Class in picard.analysis.directed
Collects InsertSizeMetrics on the specified accumulationLevels using
InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, Integer, double, boolean) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
 
InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
 
instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
For testing
instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
The main method.
instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
 
INTENSITY_ONLY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
IntensityChannel - Enum in picard.illumina.parser
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
INTERGENIC - picard.annotation.LocusFunction
 
INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary alignments that do not align to any gene.
INTERLEAVE - Variable in class picard.sam.SamToFastq
 
INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
The path to the directory containing the tile metrics file relative to the basecalling directory.
interruptAndShutdownExecutors(ThreadPoolExecutorWithExceptions...) - Method in class picard.illumina.BasecallsConverter
 
INTERSECT - picard.util.IntervalListTools.Action
 
INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
 
INTERVAL_COUNT - picard.util.IntervalList.IntervalListScatterMode
A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count.
INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER - picard.util.IntervalList.IntervalListScatterMode
A scatter by interval **count** which attempts to fill each resulting interval list with approximately equal numbers of intervals, disregarding the base count.
INTERVAL_ITERATOR - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
 
INTERVAL_LIST - Variable in class picard.sam.AddOATag
 
INTERVAL_LIST - Variable in class picard.sam.FilterSamReads
 
INTERVAL_LIST - Variable in class picard.sam.ViewSam
 
INTERVAL_SUBDIVISION - picard.util.IntervalList.IntervalListScatterMode
A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).
intervalArgumentCollection - Variable in class picard.analysis.CollectWgsMetrics
 
IntervalArgumentCollection - Interface in picard.cmdline.argumentcollections
Base interface for an interval argument collection.
IntervalListScatter - Class in picard.util.IntervalList
 
IntervalListScatter(IntervalListScatterer, IntervalList, int) - Constructor for class picard.util.IntervalList.IntervalListScatter
 
IntervalListScatterer - Interface in picard.util.IntervalList
An interface for a class that scatters IntervalLists.
IntervalListScattererByBaseCount - Class in picard.util.IntervalList
a Baseclass for scatterers that scatter by uniqued base count.
IntervalListScattererByBaseCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByBaseCount
 
IntervalListScattererByIntervalCount - Class in picard.util.IntervalList
Scatters IntervalList by interval count so that resulting IntervalList's have the same number of intervals in them.
IntervalListScattererByIntervalCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCount
 
IntervalListScattererByIntervalCountWithDistributedRemainder - Class in picard.util.IntervalList
Scatters IntervalList by into `interval count` shards so that resulting IntervalList's have approximately same number of intervals in them.
IntervalListScattererByIntervalCountWithDistributedRemainder() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
 
IntervalListScattererWithoutSubdivision - Class in picard.util.IntervalList
A BaseCount Scatterer that avoid breaking-up intervals.
IntervalListScattererWithoutSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
 
IntervalListScattererWithoutSubdivisionWithOverflow - Class in picard.util.IntervalList
Like IntervalListScattererWithoutSubdivision but will overflow current list if the projected size of the remaining lists is bigger than the "ideal".
IntervalListScattererWithoutSubdivisionWithOverflow() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
 
IntervalListScattererWithSubdivision - Class in picard.util.IntervalList
An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
IntervalListScattererWithSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithSubdivision
 
IntervalListScatterMode - Enum in picard.util.IntervalList
An enum to control the creation of the various IntervalListScatter objects
IntervalListToBed - Class in picard.util
Trivially simple command line program to convert an IntervalList file to a BED file.
IntervalListToBed() - Constructor for class picard.util.IntervalListToBed
 
IntervalListTools - Class in picard.util
Performs various IntervalList manipulations.
IntervalListTools() - Constructor for class picard.util.IntervalListTools
 
IntervalListTools.Action - Enum in picard.util
 
intervals - Variable in class picard.analysis.AbstractWgsMetricsCollector
 
intervals - Variable in class picard.analysis.WgsMetrics
The intervals over which this metric was computed.
INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
INTERVALS - Variable in class picard.analysis.CollectMultipleMetrics
 
INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
 
INTERVALS - Variable in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
 
INTERVALS - Variable in class picard.analysis.CollectWgsMetrics
 
INTERVALS - Variable in class picard.reference.NonNFastaSize
 
INTERVALS - Variable in class picard.sam.MergeSamFiles
 
INTERVALS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
INTERVALS - Variable in class picard.vcf.GenotypeConcordance
 
IntervalsManipulationProgramGroup - Class in picard.cmdline.programgroups
Tools that process genomic intervals in various formats.
IntervalsManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
 
intervalWeight(Interval) - Method in interface picard.util.IntervalList.IntervalListScatterer
A method that defines the "weight" of an interval list for the purpose of scattering.
intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
 
intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
 
INTRONIC - picard.annotation.LocusFunction
 
INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
INVERT - Variable in class picard.util.IntervalListTools
 
IO_SIZE - Variable in class picard.util.FifoBuffer
 
IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
 
IS_BISULFITE_SEQUENCE - Variable in class picard.sam.SetNmMdAndUqTags
 
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
 
IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
 
IS_MIXED - picard.vcf.GenotypeConcordanceStates.CallState
 
IS_MIXED - picard.vcf.GenotypeConcordanceStates.TruthState
 
IS_MIXED_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
IS_ZCALLED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
Whether the sample was zcalled
isAdapter(SAMRecord) - Method in class picard.analysis.AdapterUtility
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[]) - Method in class picard.analysis.AdapterUtility
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAdapterSequence(byte[], boolean) - Method in class picard.analysis.AdapterUtility
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
isAmbiguous() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
isAvailable - Variable in enum picard.nio.PathProvider
 
isBlank(byte[]) - Method in class picard.util.AbstractInputParser
Determines whether a given line is a comment
isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
 
isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
Checks whether the given read is part of a chimeric pair.
isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
Checks whether the given read is part of a chimeric pair.
isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
 
isClosed() - Method in class picard.util.CircularByteBuffer
Returns true if the buffer is closed, false otherwise.
isClusterRecord() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
 
isComment(byte[]) - Method in class picard.util.AbstractInputParser
Determines whether a given line is a comment
isContaminant(HitsForInsert) - Method in class picard.sam.AbstractAlignmentMerger
 
isContaminant(HitsForInsert) - Method in class picard.sam.SamAlignmentMerger
Criteria for contaminant reads: 1.
isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
isDelimiter(byte) - Method in class picard.util.AbstractInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.CsvInputParser
Determines whether a given character is a delimiter
isDelimiter(byte) - Method in class picard.util.TabbedInputParser
Determines whether a given character is a delimiter
isDupe() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
 
isExpected() - Method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
 
isFail() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
 
isHeterozygous() - Method in enum picard.fingerprint.DiploidGenotype
 
isHomomozygous() - Method in enum picard.fingerprint.DiploidGenotype
 
isIndel() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
isIntensityOnly() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
 
isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
 
isKeepValid() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
isLegacyPicardStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
 
isMatch() - Method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
 
isMatched() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
 
isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is MISSING.
isOpticalDuplicate - Variable in class picard.sam.markduplicates.util.ReadEnds
A *transient* flag marking this read end as being an optical duplicate.
isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
 
isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
isPf() - Method in class picard.illumina.parser.CbclData
 
isPf() - Method in class picard.illumina.parser.ClusterData
 
isPhasing(IlluminaMetricsCode) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
 
isPopulateOaTag() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
isRefStrandDefinedInManifest() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
 
isResetMappingInformation() - Method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
isSkipBlankLines() - Method in class picard.util.AbstractInputParser
 
isSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
 
isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
 
isValidBase(byte) - Static method in enum picard.fingerprint.DiploidGenotype
 
isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns true if EITHER the truth or call state is a VAR.
isVariantFile(File) - Static method in class picard.vcf.VcfUtils
Checks if the suffix is one of those that are allowed for the various formats that contain variants (currently vcf and bcf)
isWGT - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
iterator() - Method in class picard.annotation.Gene
 
iterator() - Method in class picard.arrays.illumina.IlluminaManifest
 
iterator() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
 
iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
iterator() - Method in class picard.illumina.parser.TileIndex
 
iterator() - Method in class picard.util.AbstractInputParser
 
iterator() - Method in class picard.util.IntervalList.IntervalListScatter
 
iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
Creates the iterator object.
iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
Renders the embodied regions of the VCF files in the form of CloseableIterators over VariantContexts.
Iterators - Class in picard.util
 
Iterators() - Constructor for class picard.util.Iterators
 
IUPAC_NUCLEOTIDE_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 

J

JAVASCRIPT_FILE - Variable in class picard.sam.FilterSamReads
 
JAVASCRIPT_FILE - Variable in class picard.vcf.filter.FilterVcf
 
JUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs that are duplicates
JUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
The fraction of outward-facing pairs that are marked as duplicates
JUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The estimated library size for outward-facing pairs
JUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The mean insert size for outward-facing pairs
JUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs in the SAM file
JUMP_SIZE - Variable in class picard.sam.MergeBamAlignment
Deprecated.
JUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The standard deviation on the insert size for outward-facing pairs
JumpingLibraryMetrics - Class in picard.analysis
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
JumpingLibraryMetrics() - Constructor for class picard.analysis.JumpingLibraryMetrics
 

K

KEEP_FIRST_DUPLICATE - Variable in class picard.sam.RevertSam
 
klDivergance(double[], double[]) - Static method in class picard.util.MathUtil
Calculate the KL divergence from measured to distribution // https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence

L

lane - Variable in class picard.illumina.parser.BaseIlluminaDataProvider
 
lane - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
lane - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The lane, which is determined from the file name
LANE - Variable in class picard.fastq.BamToBfq
 
LANE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
LANE - Variable in class picard.illumina.ExtractBarcodesProgram
 
LANE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The lane for which the metrics were calculated.
LANE - Variable in class picard.illumina.IlluminaLaneMetrics
This lane's number.
LANE - Variable in class picard.illumina.IlluminaPhasingMetrics
Illumina flowcell lane number
LANE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
LANE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
laneFactories - Variable in class picard.illumina.BasecallsConverter
 
laneIsSet() - Method in class picard.illumina.parser.ClusterData
 
LanePhasingMetricsCollector - Class in picard.illumina
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
LanePhasingMetricsCollector(Collection<Tile>, boolean) - Constructor for class picard.illumina.LanePhasingMetricsCollector
Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the first and second (if available) reads
LANES - Variable in class picard.illumina.CheckIlluminaDirectory
 
laneTileCode - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
 
LEFT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_FILE - Variable in class picard.sam.SamComparisonMetric
Left file used in comparison
LEFT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_PRIMER - Variable in class picard.util.BaitDesigner
 
LEFT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
 
LEFT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
 
leftAlignVariant(VariantContextBuilder, int, int, List<Allele>, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
Normalizes and left aligns a VariantContextBuilder.
leftVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
 
length - Variable in class picard.illumina.parser.Range
 
length - Variable in class picard.illumina.parser.ReadDescriptor
 
length() - Method in class picard.annotation.Gene.Transcript
 
length() - Method in class picard.illumina.parser.ReadStructure.Substructure
 
leniantHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
Deprecated.
LENIENT_DUP - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
LENIENT_HAMMING - picard.illumina.DistanceMetric
 
LENIENT_HEADER - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
LENIENT_LOW_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
LENIENT_UNKNOWN_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
lenientHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
LIBRARY - picard.analysis.MetricAccumulationLevel
 
LIBRARY - picard.fingerprint.CrosscheckMetric.DataType
 
LIBRARY - picard.sam.markduplicates.MarkDuplicates.DuplicateType
 
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The name of the library being assayed.
LIBRARY - Variable in class picard.metrics.MultilevelMetrics
The library to which these metrics apply.
LIBRARY - Variable in class picard.sam.DuplicationMetrics
The library on which the duplicate marking was performed.
LIBRARY - Variable in class picard.sam.markduplicates.UmiMetrics
Library that was used to generate UMI data.
LIBRARY_NAME - Variable in class picard.illumina.BarcodeMetric
The name of the library
LIBRARY_NAME - Variable in class picard.illumina.IlluminaBasecallsToSam
 
LIBRARY_NAME - Variable in class picard.sam.FastqToSam
 
LIBRARY_NAME - Variable in class picard.sam.RevertSam
 
LIBRARY_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
Column header for the library name.
LIBRARY_NAME_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
LIBRARY_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
libraryId - Variable in class picard.sam.markduplicates.util.ReadEnds
 
libraryIdGenerator - Variable in class picard.sam.markduplicates.MarkDuplicates
 
LibraryIdGenerator - Class in picard.sam.markduplicates.util
A class to generate library Ids and keep duplication metrics by library IDs.
LibraryIdGenerator(SAMFileHeader) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
 
LIFTOVER_FAILED - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
 
LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS - Static variable in class picard.fingerprint.LiftOverHaplotypeMap
 
LIFTOVER_MIN_MATCH - Variable in class picard.vcf.LiftoverVcf
 
LiftOverHaplotypeMap - Class in picard.fingerprint
Liftover SNPs in HaplotypeMaps from one reference to another
LiftOverHaplotypeMap() - Constructor for class picard.fingerprint.LiftOverHaplotypeMap
 
LiftOverIntervalList - Class in picard.util
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
LiftOverIntervalList() - Constructor for class picard.util.LiftOverIntervalList
 
LiftoverUtils - Class in picard.util
 
LiftoverUtils() - Constructor for class picard.util.LiftoverUtils
 
LiftoverVcf - Class in picard.vcf
Summary
LiftoverVcf() - Constructor for class picard.vcf.LiftoverVcf
 
liftSimpleVariantContext(VariantContext, Interval) - Static method in class picard.util.LiftoverUtils
 
liftVariant(VariantContext, Interval, ReferenceSequence, boolean, boolean) - Static method in class picard.util.LiftoverUtils
This will take an input VariantContext and lift to the provided interval.
limitingProcessedRegionsTo(IntervalList) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
LINE_LENGTH - Variable in class picard.reference.ExtractSequences
 
LINE_LENGTH - Variable in class picard.reference.NormalizeFasta
 
LINK_LOCS - Variable in class picard.illumina.CheckIlluminaDirectory
Deprecated.
It is no longer necessary to create locs file symlinks.
listWeight(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
A method that defines the "weight" of an interval for the purpose of scattering.
listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
 
listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
 
LL_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
The Log Likelihood of the sequence data given the expected sample's genotypes.
LL_RANDOM_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
The Log Likelihood of the sequence data given a random sample from the human population.
LLK - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
The log likelihood
LLK0 - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
The log likelihood 0
loadFingerprints(Path, String) - Method in class picard.fingerprint.FingerprintChecker
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromNonIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromQueriableReader(VCFFileReader, String, Path) - Method in class picard.fingerprint.FingerprintChecker
Loads genotypes from the supplied reader into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadFingerprintsFromVariantContexts(Iterable<VariantContext>, String, Path) - Method in class picard.fingerprint.FingerprintChecker
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
loadPropertiesFile(String, Class<?>) - Static method in class picard.util.PropertyUtils
Attempt to load a Properties object from an on-disk properties file.
loadRefFlat(File, SAMSequenceDictionary) - Static method in class picard.annotation.GeneAnnotationReader
 
LOCATION_BIN_SIZE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
Locs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
LocsFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
LocsFileFaker() - Constructor for class picard.illumina.parser.fakers.LocsFileFaker
 
LocsFileReader - Class in picard.illumina.parser.readers
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
LocsFileReader(File) - Constructor for class picard.illumina.parser.readers.LocsFileReader
 
LocsFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.LocsFileReader
 
LOCUS_ACCUMULATION_CAP - Variable in class picard.analysis.CollectWgsMetrics
 
LOCUS_MAX_READS - Variable in class picard.fingerprint.ExtractFingerprint
 
LOCUS_MAX_READS - Variable in class picard.fingerprint.IdentifyContaminant
 
LocusFunction - Enum in picard.annotation
Describes the behavior of a locus relative to a gene.
LOD - Variable in class picard.analysis.FingerprintingDetailMetrics
The LOD score for OBSERVED_GENOTYPE vs.
LOD_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
The LOD for Expected Sample vs.
LOD_SCORE - Variable in class picard.fingerprint.CrosscheckMetric
 
LOD_SCORE_NORMAL_TUMOR - Variable in class picard.fingerprint.CrosscheckMetric
 
LOD_SCORE_TUMOR_NORMAL - Variable in class picard.fingerprint.CrosscheckMetric
 
LOD_SELF_CHECK - Variable in class picard.fingerprint.FingerprintMetrics
The fingerprinting LOD score this sample gets when compared to itself (big is good)
LOD_THRESHOLD - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
 
LOD_THRESHOLD - Variable in class picard.fingerprint.CrosscheckFingerprints
 
log - Static variable in class picard.illumina.SortedBasecallsConverter
 
log - Static variable in class picard.util.LiftoverUtils
 
LOG - Static variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
LOG - Static variable in class picard.vcf.VcfFormatConverter
 
LOG - Static variable in class picard.vcf.VcfToIntervalList
 
LOG_10_MATH - Static variable in class picard.util.MathUtil
 
LOG_2_MATH - Static variable in class picard.util.MathUtil
 
LOG_4_BASE_E - Static variable in class picard.util.MathUtil
Constant to convert between the natural base e and 4.0.
LOG_FAILED_INTERVALS - Variable in class picard.vcf.LiftoverVcf
 
LOG_ODDS_THRESHOLD - Variable in class picard.analysis.TheoreticalSensitivityMetrics
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
log10_1p(double) - Static method in class picard.util.MathUtil
this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x
LOG10_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
The log10 of the Chi-squared pvalue
LOG10_HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
The log10 of the Chi-squared pvalue for the number of HETs and HOMs
LOG10_HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
LOG10_PVAL - Variable in class picard.arrays.BafRegressMetrics
The log p-value of the estimate
logLikelihoodsToProbs(double[]) - Static method in class picard.util.MathUtil
Deprecated.
logMemoryStats(Log) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
logRRatio - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
LONG_HOMOPOLYMER - picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
 
LONG_HOMOPOLYMER - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
longLaneStr(int) - Static method in class picard.illumina.parser.IlluminaFileUtil
 
LOSS_OF_HET_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
 
LOW_DP - picard.vcf.GenotypeConcordanceStates.CallState
 
LOW_DP - picard.vcf.GenotypeConcordanceStates.TruthState
 
LOW_DP_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
LOW_GQ - picard.vcf.GenotypeConcordanceStates.CallState
 
LOW_GQ - picard.vcf.GenotypeConcordanceStates.TruthState
 
LOW_GQ_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
LOW_MQ_THRESHOLD - Variable in class picard.sam.util.SAMComparisonArgumentCollection
 
LRR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 

M

M - picard.illumina.parser.ReadType
 
MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MAD_COVERAGE - Variable in class picard.analysis.WgsMetrics
The median absolute deviation of coverage of the genome after all filters are applied.
MAD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The median absolute deviation of the distribution of all read lengths.
main(String[]) - Static method in class picard.cmdline.PicardCommandLine
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
main(String[]) - Static method in class picard.sam.DuplicationMetrics
 
main(String[]) - Static method in class picard.Test
 
make() - Method in enum picard.util.IntervalList.IntervalListScatterMode
Create the scatterer
makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
 
makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
 
makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
 
makeBarcodeRegex(int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
 
makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
Make an InsertSizeCollector with the given arguments
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.GcBiasMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
 
makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectHsMetrics
 
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedMetrics
A factory method for the TargetMetricsCollector to use this time.
makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
 
makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
 
makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) - Method in class picard.illumina.parser.MultiTileBclParser
 
makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
 
makeDataProvider(Integer) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
 
makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Call this method to create a ClusterData iterator over the specified tiles.
makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Create a string that will be included in any NoSuchElementException thrown by the next() method
makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
 
makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
 
makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
 
makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>, boolean) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
By default, this method calls the CollectMultipleMetrics.ProgramInterface.makeInstance(String, String, File, File, Set, File, File, File, Set) method without 'includeUnpaired' parameter.
makeIntervalArgumentCollection() - Method in class picard.analysis.CollectWgsMetrics
 
makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
Handles the FastqToSam execution on the FastqReader(s).
makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
 
makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
Return a regex string for finding Lane and Tile given a file extension pattern
makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeOverlapDetector(File, SAMFileHeader, File, Log) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
 
makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeReferenceArgumentCollection() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
makeReferenceArgumentCollection() - Method in class picard.analysis.CollectRrbsMetrics
 
makeReferenceArgumentCollection() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
makeReferenceArgumentCollection() - Method in class picard.cmdline.CommandLineProgram
 
makeReferenceArgumentCollection() - Method in class picard.sam.CreateSequenceDictionary
 
makeReferenceArgumentCollection() - Method in class picard.sam.DownsampleSam
 
makeReferenceArgumentCollection() - Method in class picard.util.ScatterIntervalsByNs
 
makeReferenceArgumentCollection() - Method in class picard.vcf.LiftoverVcf
 
makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
 
makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
 
makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
MakeSitesOnlyVcf - Class in picard.vcf
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
 
makeSortingCollection() - Static method in class picard.util.SequenceDictionaryUtils
 
makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
Factory method for the iterator of each tile
makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
Make an CloseableIterator based on the given file and fileType specified at construction.
MakeVcfSampleNameMap - Class in picard.vcf
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
MakeVcfSampleNameMap() - Constructor for class picard.vcf.MakeVcfSampleNameMap
 
Male - picard.pedigree.Sex
 
MALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
MANIFEST_FILE_HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
 
manifestFileParser - Variable in class picard.arrays.illumina.IlluminaManifest
 
manifestName - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
MAP_FILE - Variable in class picard.arrays.MergePedIntoVcf
 
MAP_INFO_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
mappingQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the mapping-quality of the read under consideration
MAPPINGS_DIFFER - picard.sam.util.SamComparison.AlignmentComparison
 
MAPPINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
MAPPINGS_MATCH - picard.sam.util.SamComparison.AlignmentComparison
 
MAPPINGS_MATCH - Variable in class picard.sam.SamComparisonMetric
The number of primary records for which mappings match in files.
MarkDuplicates - Class in picard.sam.markduplicates
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
 
MarkDuplicates.DuplicateTaggingPolicy - Enum in picard.sam.markduplicates
Enum used to control how duplicates are flagged in the DT optional tag on each read.
MarkDuplicates.DuplicateType - Enum in picard.sam.markduplicates
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
Initializes the mark duplicates iterator.
MarkIlluminaAdapters - Class in picard.illumina
Command line program to mark the location of adapter sequences.
MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
 
MarkQueue - Class in picard.sam.markduplicates.util
This is the mark queue.
MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
 
MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
MATCHING_DICTIONARY_TAGS - Variable in class picard.sam.MergeBamAlignment
 
matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
A pattern that will match files of this type for this lane
MatchResults - Class in picard.fingerprint
Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
MathUtil - Class in picard.util
General math utilities
MathUtil.LogMath - Class in picard.util
A collection of common math operations that work with log values.
MATRIX_OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
MATRIX_OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
 
max(double[]) - Static method in class picard.util.MathUtil
Returns the largest value stored in the array.
max(long[]) - Static method in class picard.util.MathUtil
Returns the largest value stored in the array.
MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH - Static variable in class picard.cmdline.CommandLineProgram
CommandLineProgramProperties oneLineSummary attribute must be shorted than this in order to maintain reasonable help output formatting.
MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
 
MAX_EDIT_DISTANCE_TO_JOIN - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK - Variable in class picard.fingerprint.CrosscheckFingerprints
 
MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
The default value used for the maximum error rate when matching read bases to clippable sequence.
MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
 
MAX_FS - Variable in class picard.vcf.filter.FilterVcf
 
MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The maximum measure insert size by alignment.
MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
 
MAX_LOCI - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
 
MAX_MISMATCHES - Variable in class picard.illumina.ExtractBarcodesProgram
 
MAX_NO_CALLS - Variable in class picard.illumina.ExtractBarcodesProgram
 
MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
 
MAX_OPTICAL_DUPLICATE_SET_SIZE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
 
MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
The double value closest to 1 while still being less than 1.
MAX_Q - Variable in class picard.sam.FastqToSam
 
MAX_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The maximum read length.
MAX_READ_LENGTH - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
Deprecated.
MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
 
MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
 
MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
MAX_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
The maximum coverage of reads that mapped to target regions of an experiment.
MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
 
MAX_UNSIGNED_SHORT - Static variable in class picard.arrays.illumina.InfiniumDataFile
 
maximalInterestingDistance - Variable in class picard.util.BarcodeEditDistanceQuery
maximal edit distance between reads and barcodes to be considered
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
 
maybeDemultiplex(ClusterData, Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure) - Method in class picard.illumina.BasecallsConverter
If we are demultiplexing and a barcodeExtractor is defined then this method will perform on-the-fly demuxing.
mean(double...) - Method in class picard.util.MathUtil.LogMath
Computes the mean of the provided log values.
mean(double[]) - Static method in class picard.util.MathUtil
 
mean(double[], int, int) - Static method in class picard.util.MathUtil
Calculated the mean of an array of doubles.
MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
The mean read coverage of all amplicon regions in the experiment.
MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
The mean coverage of all baits in the experiment.
MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean number of clusters per tile.
MEAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
The mean coverage in bases of the genome territory, after all filters are applied.
MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
Mean coverage of CpG sites
MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The mean insert size of the "core" of the distribution.
MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean percentage of pf clusters per tile.
MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The mean number of pf clusters per tile.
MEAN_PROBE_COVERAGE - Variable in class picard.analysis.directed.TargetMetrics
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
MEAN_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The mean read length of the set of reads examined.
MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
The mean coverage of targets.
MEAN_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
MEAN_UMI_LENGTH - Variable in class picard.sam.markduplicates.UmiMetrics
Number of bases in each UMI
MEAN_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
MEAN_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
MeanQualityByCycle - Class in picard.analysis
Program to generate a data table and chart of mean quality by cycle from a BAM file.
MeanQualityByCycle - picard.analysis.CollectMultipleMetrics.Program
 
MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
 
meanR - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
meanTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
median(double...) - Static method in class picard.util.MathUtil
Calculate the median of an array of doubles.
MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript.
MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
The median absolute deviation of the distribution.
MEDIAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
The median coverage in bases of the genome territory, after all filters are applied.
MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
Median coverage of CpG sites
MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
MEDIAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The median read length.
MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
The median coverage of targets.
MemoryBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
Map from String to ReadEnds object.
MemoryBasedReadEndsForMarkDuplicatesMap() - Constructor for class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
 
MendelianViolationMetrics - Class in picard.vcf.MendelianViolations
Describes the type and number of mendelian violations found within a Trio.
MendelianViolationMetrics() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationMetrics
 
MendelianViolationsByFamily - Class in picard.vcf.MendelianViolations
Created by farjoun on 6/25/16.
MendelianViolationsByFamily() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationsByFamily
 
merge(Collection<? extends MergeableMetricBase>) - Method in class picard.analysis.MergeableMetricBase
for a collection of MergeableMetricBase, merge them all into "this" one.
merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
 
merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
 
merge(List<VariantContext>) - Static method in class picard.arrays.CombineGenotypingArrayVcfs
Merges multiple VariantContexts all for the same locus into a single hybrid.
merge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
Merge another metric into this one
merge(MergeableMetricBase) - Method in class picard.analysis.WgsMetrics
Merges the various PCT_EXC_* metrics.
merge(Fingerprint) - Method in class picard.fingerprint.Fingerprint
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
merge(FingerprintIdDetails) - Method in class picard.fingerprint.FingerprintIdDetails
 
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
Merges in the likelihood information from the supplied haplotype probabilities object.
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
 
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
 
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
Merges information from another haplotype probabilities object for the same haplotype into this object.
merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
 
merge(BarcodeMetric) - Method in class picard.illumina.BarcodeMetric
Adds the non-calculated
merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Adds the non-calculated fields from the other metric to this one.
MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
 
MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
 
MergeableMetricBase - Class in picard.analysis
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (MergeByAdding).
MergeableMetricBase() - Constructor for class picard.analysis.MergeableMetricBase
 
MergeableMetricBase.MergeByAdding - Annotation Type in picard.analysis
Metrics whose values can be merged by adding.
MergeableMetricBase.MergeByAssertEquals - Annotation Type in picard.analysis
Metrics whose values should be equal when merging.
MergeableMetricBase.MergingIsManual - Annotation Type in picard.analysis
Metrics that are merged manually in the MergeableMetricBase.merge(MergeableMetricBase) ()}.
MergeableMetricBase.NoMergingIsDerived - Annotation Type in picard.analysis
Metrics that are not merged, but are subsequently derived from other metrics, for example by MergeableMetricBase.calculateDerivedFields().
MergeableMetricBase.NoMergingKeepsValue - Annotation Type in picard.analysis
Metrics that are not merged.
mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
Merges the alignment data with the non-aligned records from the source BAM file.
mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
Merges the alignment from the map file with the non-aligned records from the source BAM file.
MergeBamAlignment - Class in picard.sam
Summary
MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
 
mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) - Static method in class picard.fingerprint.Fingerprint
 
mergeIfCan(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
Merges another MergableMetricBase if possible
MergePedIntoVcf - Class in picard.arrays
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
MergePedIntoVcf() - Constructor for class picard.arrays.MergePedIntoVcf
 
MergeSamFiles - Class in picard.sam
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
 
MergeVcfs - Class in picard.vcf
Combines multiple variant files into a single variant file.
MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectInsertSizeMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectMultipleMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRnaSeqMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
 
METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
METRIC_ALLOWABLE_RELATIVE_CHANGE - Variable in class picard.analysis.CompareMetrics
 
MetricAccumulationLevel - Enum in picard.analysis
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
metrics - Variable in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
 
METRICS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
 
METRICS_FILE - Variable in class picard.sam.DownsampleSam
 
METRICS_FILE - Variable in class picard.sam.markduplicates.CollectDuplicateMetrics
 
METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
 
METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
METRICS_TO_IGNORE - Variable in class picard.analysis.CompareMetrics
 
MetricToAllowableRelativeChange - Variable in class picard.analysis.CompareMetrics
 
min(byte[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
min(double[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
min(int[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
min(short[]) - Static method in class picard.util.MathUtil
Returns the smallest value stored in the array.
MIN_AB - Variable in class picard.vcf.filter.FilterVcf
 
MIN_BASE_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
MIN_DP - Variable in class picard.vcf.filter.FilterVcf
 
MIN_DP - Variable in class picard.vcf.GenotypeConcordance
 
MIN_DP - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
 
MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
 
MIN_GQ - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
MIN_GROUP_COUNT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MIN_HET_FRACTION - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
MIN_HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
 
MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The minimum measured insert size.
MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
 
MIN_MAPPING_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
The default value used for the minimum number of contiguous bases to match against.
MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
 
MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
The default value used for the minimum number of contiguous bases to match against in a paired end read
MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractBarcodesProgram
 
MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
MIN_Q - Variable in class picard.sam.FastqToSam
 
MIN_QD - Variable in class picard.vcf.filter.FilterVcf
 
MIN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The minimum read length.
MIN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
The minimum coverage of reads that mapped to target regions of an experiment.
MIN_TRIMMED_LENGTH - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
MIN_UNCLIPPED_BASES - Variable in class picard.sam.MergeBamAlignment
 
MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
 
MINIMUM_BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
 
MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
 
MINIMUM_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
 
MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
 
MINIMUM_GQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
 
MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
 
MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
MINIMUM_MQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
 
MINIMUM_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
 
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
 
MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
 
minimumBaseQuality - Variable in class picard.util.BarcodeEditDistanceQuery
minimal base quality to condiser informative
MINUS - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
 
MISALIGNED - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
 
mismatchesInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
MismatchesInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
 
MISSING - picard.vcf.GenotypeConcordanceStates.CallState
 
MISSING - picard.vcf.GenotypeConcordanceStates.TruthState
 
MISSING_ALLELE_B_PROBESEQ - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Manifest contained no allele B probe sequence
MISSING_CODE - picard.vcf.GenotypeConcordanceStateCodes
These codes allow for constants in the truth state enum and the call state enum to be compared.
MISSING_LEFT - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are found in right file but not found in left file
MISSING_RIGHT - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are found in left file but not found in right file
MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
 
MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
 
MODE - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
 
MODE - Variable in class picard.sam.ValidateSamFile
 
MODE_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
The barcode name for which the metrics were calculated.
MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
The barcode sequence for which the metrics were calculated.
MOLECULAR_IDENTIFIER_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
 
MOLECULAR_INDEX_BASE_QUALITY_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
 
MOLECULAR_INDEX_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
 
molecularBarcode - Variable in class picard.illumina.parser.ReadStructure
 
MolecularIndex - Static variable in enum picard.illumina.parser.ReadType
 
MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
 
MOTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The ID of the mother within the trio.
MOVE_TO_TAG - picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
 
MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,​Histogram_KEY extends Comparable,​ARGTYPE> - Class in picard.metrics
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
 
MultilevelMetrics - Class in picard.metrics
 
MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
 
MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
multiply(double[], double[]) - Static method in class picard.util.MathUtil
Calculates the product of two arrays of the same length.
MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
MultiTileBcl - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
 
MultiTileBclFileUtil - Class in picard.illumina.parser
NextSeq-style bcl's have all tiles for a cycle in a single file.
MultiTileBclParser - Class in picard.illumina.parser
Parse .bcl.bgzf files that contain multiple tiles in a single file.
MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
 
MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_.bci file can be used to figure out where each tile starts and ends.
MultiTileFilter - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
MultiTileFilterParser - Class in picard.illumina.parser
Read filter file that contains multiple tiles in a single file.
MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
 
MultiTileLocs - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
 
MultiTileLocsParser - Class in picard.illumina.parser
Read locs file that contains multiple tiles in a single file.
MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
 
MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
Abstract class for files with fixed-length records for multiple tiles, e.g.
MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser
 

N

n - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
N - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
N_CYCLES - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
NA - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
NA - Static variable in class picard.vcf.GenotypeConcordanceScheme
These are convenience variables for defining a scheme.
nAlternateAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of doubletons where the two reads matched the alternate.
nAlternateAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of tripletons where the two reads matched the alternate.
nAlternateReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of alternate alleles in the reads.
name - Variable in class picard.annotation.Gene.Transcript
 
NAME - Variable in class picard.util.FifoBuffer
 
NAME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
NATURAL_LOG_MATH - Static variable in class picard.util.MathUtil
 
nBadBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
NCBI_35 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
NCBI_36 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
NCBI_37 - Static variable in class picard.arrays.illumina.IlluminaManifest
 
nDeletedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
Total number of deleted bases
nDeletions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
Total number of deletions
nDifferentAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of doubletons where the two reads had different bases in the locus.
nDifferentAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of tripletons where at least one of the reads didn't match either allele of the het site.
nDuplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of duplicate sets examined.
NEAR_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
NEAR_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
NEAR_DISTANCE - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
NEAR_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
NEAR_PROBE_DISTANCE_DEFAULT - Static variable in class picard.analysis.directed.TargetMetricsCollector
Default distance for a read to be considered "selected".
needsReferenceSequence() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
needsRefflatFile() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
NEGATIVE - picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
 
NEW_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
 
newCounter() - Method in class picard.analysis.CounterManager
Creates a new Counter object and adds it to the list of managed Counters.
nExactlyDouble - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of sets of size exactly 2 found.
nExactlyTriple - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of sets of size exactly 3 found.
next() - Method in class picard.illumina.parser.MultiTileParser
 
next() - Method in class picard.illumina.parser.PerTileParser
 
next() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Return the next set of coordinates in a given file.
next() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
next() - Method in class picard.illumina.parser.readers.BclReader
 
next() - Method in class picard.illumina.parser.readers.CbclReader
 
next() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
 
next() - Method in class picard.illumina.parser.readers.FilterFileReader
 
next() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
next() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
next() - Method in class picard.util.AsyncIterator
 
next() - Method in interface picard.util.AtomicIterator
Produces the next element from the iterator, if there is one; otherwise, produces Optional.EMPTY
next() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
next() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
next() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
next() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
next() - Method in class picard.vcf.PairedVariantSubContextIterator
 
next() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
NEXT_BASE_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
 
NEXTERA_V1 - picard.util.IlluminaUtil.IlluminaAdapterPair
 
NEXTERA_V2 - picard.util.IlluminaUtil.IlluminaAdapterPair
 
nextReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.
nGoodBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
the number of sets where the UMIs had good quality bases and were used for any comparisons.
NHOM - Variable in class picard.arrays.BafRegressMetrics
The number of homozygous genotypes used to fit the model
nInsertedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
Total number of inserted bases
nInsertions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
Total number of inserts
nMatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of UMIs that are match within Bi-sets that come from different alleles.
nMatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of UMIs that are match within Bi-sets that come from the same alleles.
nMismatchingAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of tripletons where the two reads had different bases in the locus.
nMismatchingAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of tripletons where at least one of the reads didn't match either allele of the het site.
nMismatchingBases - Variable in class picard.sam.SamErrorMetric.SimpleErrorCalculator
 
nMismatchingUMIsInContraOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of bi-sets with mismatching UMIs and opposite orientation.
nMismatchingUMIsInCoOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of bi-sets with mismatching UMIs and same orientation.
nMismatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of UMIs that are different within Bi-sets that come from different alleles.
nMismatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of UMIs that are different within Bi-sets that come from the same alleles.
NN - picard.arrays.illumina.IlluminaGenotype
 
NO_CALL - picard.vcf.GenotypeConcordanceStates.CallState
 
NO_CALL - picard.vcf.GenotypeConcordanceStates.TruthState
 
NO_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
 
NO_CALL_BASE - Static variable in class picard.illumina.parser.readers.BaseBclReader
 
NO_CALL_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
NO_LIBRARIES_SPECIFIED_IN_HEADER - Static variable in class picard.sam.SplitSamByLibrary
 
NO_MATCH - Static variable in class picard.util.ClippingUtility
The value returned by methods returning int when no match is found.
NO_PHENO - Static variable in class picard.pedigree.PedFile
 
NO_VALUE - Static variable in interface picard.sam.util.PhysicalLocation
 
noMatchMetric - Variable in class picard.illumina.ExtractBarcodesProgram
 
NON_CPG_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of times a non-CpG cytosine was encountered
NON_CPG_CONVERTED_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
NON_REF_GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The non-ref genotype concordance, ie for all var states only.
NON_ZERO_REGIONS - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
 
NONE - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
 
NONE - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
 
NONJUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pais that are duplicates
NONJUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
The fraction of inward-facing pairs that are marked as duplicates
NONJUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The estimated library size for inward-facing pairs
NONJUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The mean insert size for inward-facing pairs
NONJUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pairs in the SAM file
NONJUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
The standard deviation on the insert size for inward-facing pairs
NonNFastaSize - Class in picard.reference
A tool to count the number of non-N bases in a fasta file
NonNFastaSize() - Constructor for class picard.reference.NonNFastaSize
 
NonPF - picard.sam.ViewSam.PfStatus
 
nonSkips - Variable in class picard.illumina.parser.ReadStructure
 
nonStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
A constant stratifier which places all the reads into a single stratum.
normalizationVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
normalizeAlleles(VariantContext, String, VariantContext, String, Boolean) - Static method in class picard.vcf.GenotypeConcordance
Gets the alleles for the truth and call genotypes.
NORMALIZED_COVERAGE - Variable in class picard.analysis.GcBiasDetailMetrics
The ratio of "coverage" in this GC bin vs.
normalizedXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
normalizedYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
NormalizeFasta - Class in picard.reference
Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
NormalizeFasta() - Constructor for class picard.reference.NormalizeFasta
 
normalizeHistogram(Histogram<Integer>) - Static method in class picard.analysis.TheoreticalSensitivity
 
NORMX - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
NORMY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
NOT_ALIGNED_ERROR - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
 
NotReported - picard.pedigree.Sex
 
NOVEL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing indels called that were not found in dbSNP
NOVEL_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
NOVEL_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of high confidence SNPS called that were not found in dbSNP
NOVEL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing bi-allelic SNPS called that were not found in dbSNP
NOVEL_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
nReadsInBigSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of reads in duplicate of sizes greater than 3.
nRecordsInMemory - Variable in class picard.annotation.SortGff
 
nReferenceAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of doubletons where the two reads matched the reference.
nReferenceAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of tripletons where the two reads matched the reference.
nReferenceReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The number of reference alleles in the reads.
nsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratify by the number of Ns found in the read.
NsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
 
nSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The count of sites used.
nThreeAllelesSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The count of sites in which a third allele was found.
nTotalReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
The total number of reads over the het sites.
NUM_ADAPTERS_TO_KEEP - Variable in class picard.illumina.MarkIlluminaAdapters
 
NUM_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The total number of assays (SNP and indels) in the VCF
NUM_AUTOCALL_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of passing autocall calls
NUM_BASES_WITH_OVERLAPPING_READS - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The number of bases for which an overlapping base from the mate read was found
NUM_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of passing calls
NUM_CHANNELS - Static variable in enum picard.illumina.parser.IntensityChannel
 
NUM_DELETED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The number of deleted bases.
NUM_DELETIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The number of deletions.
NUM_DIPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of diploid sites at which a potential de-novo mutation was observed (i.e.
NUM_DISAGREES_WITH_REF_AND_MATE - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The number of bases that disagree with both the reference and their mate (which agree with each other)
NUM_DISAGREES_WITH_REFERENCE_ONLY - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The number of bases that disagree with the reference, but agree with their mate
NUM_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The total number of filtered assays in the VCF
NUM_HAPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
NUM_HAPLOID_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
NUM_HET - Variable in class picard.fingerprint.FingerprintMetrics
Number of heterozygous calls
NUM_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
Number of major allele homozygous calls
NUM_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
Number of minor allele homozygous calls
NUM_HOM_ANY - Variable in class picard.fingerprint.FingerprintMetrics
Number of homozygous calls of either allele (might not be the sum of FingerprintMetrics.NUM_HOM_ALLELE1 and FingerprintMetrics.NUM_HOM_ALLELE1 due to rounding
NUM_HOM_HET_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
NUM_HOMREF_HOMVAR_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
NUM_HOMVAR_HOMVAR_HET - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
NUM_IN_DB_SNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of high confidence SNPs found in dbSNP
NUM_IN_DB_SNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing bi-allelic SNPs found in dbSNP
NUM_IN_DB_SNP_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing complex indels found in dbSNP
NUM_IN_DB_SNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing indels found in dbSNP
NUM_IN_DB_SNP_MULTIALLELIC - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing multi-allelic SNPs found in dbSNP
NUM_INDELS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of indel calls
NUM_INSERTED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The number of inserted bases.
NUM_INSERTIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
The number of insertions.
NUM_MARKERS_FILE - Variable in class picard.arrays.VcfToAdpc
 
NUM_N - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The number of Ns found in this read
NUM_NO_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of no-calls
NUM_NON_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The total number of NON-filtered assays in the VCF
NUM_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of otherwise unclassified events.
NUM_PROCESSORS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
NUM_PROCESSORS - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
NUM_PROCESSORS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
NUM_Q_GT_TWO - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The number of Quality scores greater than 2 found in this read
NUM_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
NUM_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
NUM_SEQUENCES - Variable in class picard.sam.CreateSequenceDictionary
 
NUM_SINGLETONS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
For summary metrics, the number of variants that appear in only one sample.
NUM_SINGLETONS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
For summary metrics, the number of variants that appear in only one sample.
NUM_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The number of bi-allelic SNP calls
NUM_THREADS - Variable in class picard.fingerprint.CrosscheckFingerprints
 
NUM_THREE_WAYS_DISAGREEMENT - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The number of bases that disagree with both the reference and their mate (which also disagree)
NUM_UNEXPLAINED_READS - Variable in class picard.analysis.RnaSeqMetrics
The fraction of reads for which the transcription strand model could not be inferred.
NUM_VARIANT_SITES - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
NUM_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
NUMBER_OF_SAMPLING - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
numClusters - Variable in class picard.illumina.parser.readers.FilterFileReader
The number of cluster's pf values stored in this file
numCodes - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
numOutputReads() - Method in class picard.illumina.parser.OutputMapping
 
numProcessors(int) - Method in class picard.illumina.BasecallsConverterBuilder
Configures how many processors this converter will use.

O

OBS_A - Variable in class picard.analysis.FingerprintingDetailMetrics
The number of observations of the first, or A, allele of the SNP in the sequencing data.
OBS_B - Variable in class picard.analysis.FingerprintingDetailMetrics
The number of observations of the second, or B, allele of the SNP in the sequencing data.
obsAllele1 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
obsAllele2 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
obsAlleleOther - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
 
OBSERVED_BASE_ERRORS - Variable in class picard.sam.markduplicates.UmiMetrics
Number of errors inferred by comparing the observed and inferred UMIs
OBSERVED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
OBSERVED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
 
OBSERVED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.
OBSERVED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
Number of different UMI sequences observed
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
 
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
 
of(SAMRecord) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
 
OFF_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
OFF_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF_BASES_ALIGNED that are mapped away from any baited region.
OFF_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
The number of PF aligned bases that mapped to neither on or near a probe.
OFFSPRING - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The ID of the offspring within the trio.
OFFSPRING_SEX - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The sex of the offspring.
OLD_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
 
ON_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
ON_AMPLICON_VS_SELECTED - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
ON_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
ON_BAIT_VS_SELECTED - Variable in class picard.analysis.directed.HsMetrics
The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
ON_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
The number of PF aligned probed bases that mapped to a baited region of the genome.
ON_PROBE_VS_SELECTED - Variable in class picard.analysis.directed.TargetMetrics
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
ON_TARGET_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
The number of PF aligned bases that mapped to a targeted region of the genome.
ON_TARGET_FROM_PAIR_BASES - Variable in class picard.analysis.directed.TargetMetricsBase
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
The number of all reads matching this barcode that matched with 1 error or no-call.
oneBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
openInputs(boolean) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Since this may read its inputs more than once this method does all the opening and checking of the inputs.
OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
opticalDuplicateFinder - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
OpticalDuplicateFinder - Class in picard.sam.markduplicates.util
Contains methods for finding optical/co-localized/sequencing duplicates.
OpticalDuplicateFinder() - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
Uses the default duplicate distance OpticalDuplicateFinder.DEFAULT_OPTICAL_DUPLICATE_DISTANCE (100) and the default read name regex ReadNameParser.DEFAULT_READ_NAME_REGEX.
OpticalDuplicateFinder(String, int, long, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalDuplicateFinder(String, int, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
opticalDuplicatePixelDistance - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
 
OpticalOnly - picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
 
OptionalReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
Picard default argument collection for an optional reference.
OptionalReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
 
orientation - Variable in class picard.sam.markduplicates.util.ReadEnds
 
orientationForOpticalDuplicates - Variable in class picard.sam.markduplicates.util.ReadEnds
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
ORIGINAL_ALLELES - Static variable in class picard.vcf.LiftoverVcf
Attribute used to store the list of original alleles (including REF), in the original order prior to liftover.
ORIGINAL_CONTIG - Static variable in class picard.vcf.LiftoverVcf
Attribute used to store the name of the source contig/chromosome prior to liftover.
ORIGINAL_START - Static variable in class picard.vcf.LiftoverVcf
Attribute used to store the position of the variant on the source contig prior to liftover.
ORIGINAL_VCF - Variable in class picard.arrays.MergePedIntoVcf
 
OtherProgramGroup - Class in picard.cmdline.programgroups
Miscellaneous tools, e.g.
OtherProgramGroup() - Constructor for class picard.cmdline.programgroups.OtherProgramGroup
 
out - Variable in class picard.sam.FixMateInformation
 
out - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
out - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
OUT_PREFIX - Variable in class picard.sam.SplitSamByNumberOfReads
 
output - Variable in class picard.analysis.SinglePassSamProgram
 
OUTPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
OUTPUT - Variable in class picard.analysis.CollectMultipleMetrics
 
OUTPUT - Variable in class picard.analysis.CollectOxoGMetrics
 
OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
 
OUTPUT - Variable in class picard.analysis.CompareMetrics
 
OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
OUTPUT - Variable in class picard.analysis.SinglePassSamProgram
 
OUTPUT - Variable in class picard.annotation.SortGff
 
OUTPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
OUTPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
 
OUTPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
 
OUTPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
 
OUTPUT - Variable in class picard.arrays.GtcToVcf
 
OUTPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
 
OUTPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
OUTPUT - Variable in class picard.arrays.MergePedIntoVcf
 
OUTPUT - Variable in class picard.arrays.VcfToAdpc
 
OUTPUT - Variable in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
 
OUTPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
 
OUTPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
 
OUTPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
 
OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
 
OUTPUT - Variable in class picard.fingerprint.ExtractFingerprint
 
OUTPUT - Variable in class picard.fingerprint.IdentifyContaminant
 
OUTPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
 
OUTPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
OUTPUT - Variable in class picard.illumina.IlluminaBasecallsToSam
 
OUTPUT - Variable in class picard.illumina.MarkIlluminaAdapters
 
OUTPUT - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
OUTPUT - Variable in class picard.reference.ExtractSequences
 
OUTPUT - Variable in class picard.reference.NonNFastaSize
 
OUTPUT - Variable in class picard.reference.NormalizeFasta
 
OUTPUT - Variable in class picard.sam.AddCommentsToBam
 
OUTPUT - Variable in class picard.sam.AddOATag
 
OUTPUT - Variable in class picard.sam.AddOrReplaceReadGroups
 
OUTPUT - Variable in class picard.sam.BuildBamIndex
 
OUTPUT - Variable in class picard.sam.CalculateReadGroupChecksum
 
OUTPUT - Variable in class picard.sam.CleanSam
 
OUTPUT - Variable in class picard.sam.CompareSAMs
 
OUTPUT - Variable in class picard.sam.CreateSequenceDictionary
 
OUTPUT - Variable in class picard.sam.DownsampleSam
 
OUTPUT - Variable in class picard.sam.FastqToSam
 
OUTPUT - Variable in class picard.sam.FilterSamReads
 
OUTPUT - Variable in class picard.sam.FixMateInformation
 
OUTPUT - Variable in class picard.sam.GatherBamFiles
 
OUTPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
 
OUTPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
OUTPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
OUTPUT - Variable in class picard.sam.MergeBamAlignment
 
OUTPUT - Variable in class picard.sam.MergeSamFiles
 
OUTPUT - Variable in class picard.sam.PositionBasedDownsampleSam
 
OUTPUT - Variable in class picard.sam.ReorderSam
 
OUTPUT - Variable in class picard.sam.ReplaceSamHeader
 
OUTPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
OUTPUT - Variable in class picard.sam.RevertSam
 
OUTPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
OUTPUT - Variable in class picard.sam.SamFormatConverter
 
OUTPUT - Variable in class picard.sam.SetNmMdAndUqTags
 
OUTPUT - Variable in class picard.sam.SortSam
 
OUTPUT - Variable in class picard.sam.SplitSamByLibrary
 
OUTPUT - Variable in class picard.sam.SplitSamByNumberOfReads
 
OUTPUT - Variable in class picard.sam.ValidateSamFile
 
OUTPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
 
OUTPUT - Variable in class picard.util.BedToIntervalList
 
OUTPUT - Variable in class picard.util.IntervalListToBed
 
OUTPUT - Variable in class picard.util.IntervalListTools
 
OUTPUT - Variable in class picard.util.LiftOverIntervalList
 
OUTPUT - Variable in class picard.util.ScatterIntervalsByNs
 
OUTPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
 
OUTPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
OUTPUT - Variable in class picard.vcf.filter.FilterVcf
 
OUTPUT - Variable in class picard.vcf.FixVcfHeader
 
OUTPUT - Variable in class picard.vcf.GatherVcfs
 
OUTPUT - Variable in class picard.vcf.GenotypeConcordance
 
OUTPUT - Variable in class picard.vcf.LiftoverVcf
 
OUTPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
 
OUTPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
 
OUTPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
OUTPUT - Variable in class picard.vcf.MergeVcfs
 
OUTPUT - Variable in class picard.vcf.RenameSampleInVcf
 
OUTPUT - Variable in class picard.vcf.SortVcf
 
OUTPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
OUTPUT - Variable in class picard.vcf.VcfFormatConverter
 
OUTPUT - Variable in class picard.vcf.VcfToIntervalList
 
OUTPUT_AGILENT_FILES - Variable in class picard.util.BaitDesigner
 
OUTPUT_ALL_ROWS - Variable in class picard.vcf.GenotypeConcordance
 
OUTPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
OUTPUT_BY_READGROUP - Variable in class picard.sam.RevertSam
 
OUTPUT_BY_READGROUP_FILE_FORMAT - Variable in class picard.sam.RevertSam
 
OUTPUT_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
 
OUTPUT_DIR - Variable in class picard.sam.SamToFastq
 
OUTPUT_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
OUTPUT_DIRECTORY - Variable in class picard.util.BaitDesigner
 
OUTPUT_ERRORS_ONLY - Variable in class picard.fingerprint.CrosscheckFingerprints
 
OUTPUT_FILE_PREFIX - Variable in class picard.fastq.BamToBfq
 
OUTPUT_MAP - Variable in class picard.sam.RevertSam
 
OUTPUT_PER_RG - Variable in class picard.sam.SamToFastq
 
OUTPUT_PREFIX - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
OUTPUT_PREFIX - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
OUTPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
OUTPUT_TYPE - Variable in class picard.util.ScatterIntervalsByNs
 
OUTPUT_VALUE - Variable in class picard.util.IntervalListTools
 
OUTPUT_VCF - Variable in class picard.vcf.GenotypeConcordance
 
OUTPUT_VCF_CALL_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
 
OUTPUT_VCF_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
OUTPUT_VCF_TRUTH_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
 
OutputArgumentCollection - Interface in picard.cmdline.argumentcollections
Base interface for an output argument collection.
outputDetailMetricsFile(VariantContext.Type, MetricsFile<GenotypeConcordanceDetailMetrics, ?>, GenotypeConcordanceCounts, String, String, boolean, boolean) - Static method in class picard.vcf.GenotypeConcordance
Outputs the detailed statistics tables for SNP and Indel match categories.
OutputMapping - Class in picard.illumina.parser
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
OutputMapping(ReadStructure) - Constructor for class picard.illumina.parser.OutputMapping
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
outputMetrics() - Method in class picard.illumina.ExtractBarcodesProgram
 
OverlappingErrorMetric - Class in picard.sam.SamErrorMetric
An error metric for the errors invovling bases in the overlapping region of a read-pair.
OverlappingErrorMetric() - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
 
OverlappingErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
 
OverlappingReadsErrorCalculator - Class in picard.sam.SamErrorMetric
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
OverlappingReadsErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
 
OVERLAPS - picard.util.IntervalListTools.Action
 
OXIDATION_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
OXIDATION_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-10 * log10(OXIDATION_ERROR_RATE)
OXOG_METRICS_EXT - Static variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
OXOG_OUT - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 

P

P_95_GREEN - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
P_95_RED - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
P95_GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The 95th Intensity Percentile for the green color channel for this sample
P95_RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The 95th Intensity Percentile for the red color channel for this sample
PADDING - Variable in class picard.util.BaitDesigner
 
PADDING - Variable in class picard.util.IntervalListTools
 
Pair<X extends Comparable<X>,​Y extends Comparable<Y>> - Class in picard.sam.util
Simple Pair class.
Pair(X, Y) - Constructor for class picard.sam.util.Pair
 
PAIR - picard.analysis.AlignmentSummaryMetrics.Category
 
PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
The pair orientation of the reads in this data category.
PAIRED_END - picard.util.IlluminaUtil.IlluminaAdapterPair
The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.
PAIRED_RUN - Variable in class picard.fastq.BamToBfq
 
PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
 
PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
Deprecated.
PairedVariantSubContextIterator - Class in picard.vcf
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
PairedVariantSubContextIterator(Iterator<VariantContext>, String, Iterator<VariantContext>, String, SAMSequenceDictionary) - Constructor for class picard.vcf.PairedVariantSubContextIterator
 
PairedVariantSubContextIterator.VcfTuple - Class in picard.vcf
Little class to hold a pair of VariantContexts that are in sync with one another.
PairStratifier(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<R>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
 
PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<S>, String) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
A factory for generating "pair" stratifier instances from two stratifiers and a string
PanelMetricsBase - Class in picard.analysis.directed
A base class for Metrics for targeted panels.
PanelMetricsBase() - Constructor for class picard.analysis.directed.PanelMetricsBase
 
PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
 
ParameterizedFileUtil - Class in picard.illumina.parser
 
ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
 
parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
 
parseClusterRecordsFromTileMetrics(Collection<File>, Map<Integer, File>, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
 
parseDirective(String) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
Parses a "Directive" of the form "ERROR,STRATIFIER,STRATIFIER...etc." into a BaseErrorAggregation consisting of the appropriate BaseCalculator and the CollectionStratifier constructed from the various individual stratifiers.
parseInputFile(File, ReadStructure) - Static method in class picard.illumina.ExtractBarcodesProgram
Parses any one of the following types of files: ExtractIlluminaBarcodes BARCODE_FILE IlluminaBasecallsToFastq MULTIPLEX_PARAMS IlluminaBasecallsToSam LIBRARY_PARAMS This will validate to file format as well as populate a Map of barcodes to metrics.
parseTileMetrics(File, ReadStructure, ValidationStringency) - Static method in class picard.illumina.parser.TileMetricsUtil
Returns an unmodifiable collection of tile data read from the provided file.
PASS - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
The record in the manifest passes validation and will be used in VCF generation
PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
The "PASS"ing filter String.
PathProvider - Enum in picard.nio
A class whose purpose is to initialize the various plugins that provide Path support.
PCT_100X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
PCT_10X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
PCT_15X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
PCT_1X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
PCT_20X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
PCT_25X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
PCT_30X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
PCT_40X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
PCT_50X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
PCT_5X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
PCT_60X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
PCT_70X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
PCT_80X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
PCT_90X - Variable in class picard.analysis.WgsMetrics
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of PF reads that are unaligned or aligned with MQ0 and match to a known adapter sequence right from the start of the read (indication of adapter-dimer pairs).
PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
PCT_DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
The fraction of high confidence SNPs in dbSNP
PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The fraction of passing bi-allelic SNPs in dbSNP
PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The fraction of passing indels in dbSNP
PCT_EXC_ADAPTER - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
PCT_EXC_ADAPTER - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
PCT_EXC_BASEQ - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases that were filtered out because they were of low base quality.
PCT_EXC_BASEQ - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
PCT_EXC_CAPPED - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
PCT_EXC_DUPE - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_DUPE - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
PCT_EXC_MAPQ - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
PCT_EXC_MAPQ - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases that were filtered out because they did not align over a target base.
PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_OVERLAP - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
PCT_EXC_TOTAL - Variable in class picard.analysis.WgsMetrics
The total fraction of aligned bases excluded due to all filters.
PCT_EXC_UNPAIRED - Variable in class picard.analysis.WgsMetrics
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
The percentage of variants in a particular sample that have a GQ score of 0.
PCT_HARDCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of PF bases that are (on primary, aligned reads and) hard-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
The fraction of all reads in the lane that matched to this barcode.
PCT_MIX - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
The percent mixture (contamination) of the sample for ID
PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
PCT_OFF_PROBE - Variable in class picard.analysis.directed.TargetMetrics
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of PF_READS
PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of reads that are PF (PF_READS / TOTAL_READS)
PCT_PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of reads passing filter, PF_READS/TOTAL_READS.
PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
The percentage of PF reads that aligned to the reference sequence.
PCT_PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).
PCT_PF_UQ_READS - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
PCT_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
PCT_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of aligned reads whose mate pair was also aligned to the reference.
PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
PCT_SELECTED_BASES - Variable in class picard.analysis.directed.TargetMetrics
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
PCT_SOFTCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
the fraction of PF bases that are on (primary) aligned reads and are soft-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
PCT_TARGET_BASES_100000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 100000X or greater coverage.
PCT_TARGET_BASES_10000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 10000X or greater coverage.
PCT_TARGET_BASES_1000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 1000X or greater coverage.
PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 100X or greater coverage.
PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 10X or greater coverage.
PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 1X or greater coverage.
PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 20X or greater coverage.
PCT_TARGET_BASES_25000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 25000X or greater coverage.
PCT_TARGET_BASES_2500X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 2500X or greater coverage.
PCT_TARGET_BASES_250X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 250X or greater coverage.
PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 2X or greater coverage.
PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 30X or greater coverage.
PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 40X or greater coverage.
PCT_TARGET_BASES_50000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 50000X or greater coverage.
PCT_TARGET_BASES_5000X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 5000X or greater coverage.
PCT_TARGET_BASES_500X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 500X or greater coverage.
PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of all target bases achieving 50X or greater coverage.
PCT_UMI_WITH_N - Variable in class picard.sam.markduplicates.UmiMetrics
The percentage of reads that contain an UMI that contains at least one N
PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
The number of aligned, de-duped, on-bait bases out of the PF bases available.
PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
The number of aligned, de-duped, on-target bases out of all of the PF bases available.
PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
PED_FILE - Variable in class picard.arrays.MergePedIntoVcf
 
PedFile - Class in picard.pedigree
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
PedFile(boolean) - Constructor for class picard.pedigree.PedFile
 
PedFile.PedTrio - Class in picard.pedigree
 
PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
Constructs a TRIO that cannot be modified after the fact.
peek() - Method in class picard.sam.markduplicates.util.MarkQueue
Returns the first element in this queue
PER_BASE_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
 
PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
The fraction of mapped sequence that is marked as duplicate.
percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
Obtains percentage of two Longs
PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
The number of all reads matching this barcode that matched with 0 errors or no-calls.
permute(double[], RandomDataGenerator) - Static method in class picard.util.MathUtil
permute the input array randomly (using a RandomDataGenerator)
PerTileBarcodeExtractor(int, File, IlluminaDataProviderFactory, BarcodeExtractor) - Constructor for class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
Constructor
PerTileFileUtil - Class in picard.illumina.parser
 
PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
 
PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
 
PerTileOrPerRunFileUtil - Class in picard.illumina.parser
 
PerTileOrPerRunFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileOrPerRunFileUtil
 
PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
 
PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
 
PerTilePerCycleFileUtil - Class in picard.illumina.parser
 
PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
 
PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
 
PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
 
PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable,​ARGTYPE> - Interface in picard.metrics
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
PerUnitRnaSeqMetricsCollector(String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
 
PerUnitRnaSeqMetricsCollector(RnaSeqMetrics, String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
Derived classes that need to capture some additional metrics can use this ctor to supply a metrics instance that is a subclass of RnaSeqMetrics.
PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean, boolean) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
PF - picard.illumina.parser.IlluminaDataType
 
PF - picard.sam.ViewSam.PfStatus
 
PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
The total number of aligned PF bases.
PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of bases in all PF reads
PF_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
The number of bases in the PF_READS of a SAM or BAM file
PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
The total number of PF bases including non-aligned reads.
PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of passing-filter bases assigned to the index.
PF_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of PF clusters assigned to the index.
PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed empty.
PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed "misaligned".
PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that are deemed multiclonal.
PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile.
PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The number of non-PF reads in this tile that have not been classified.
PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of bases aligned to the reference sequence in reads that were mapped at high quality.
PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The fraction of bases that mismatch the reference in PF HQ aligned reads.
PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.
PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of insertion and deletion events per 100 aligned bases.
PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that are marked as noise reads.
PF_NORMALIZED_MATCHES - Variable in class picard.illumina.BarcodeMetric
The "normalized" matches to each barcode.
PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
The number of PF reads matching this barcode that matched with 1 error or no-call.
PF_PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
The fraction of PF reads in the lane that matched to this barcode.
PF_PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 20 or higher
PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The sum of quality scores of all bases in PF reads divided by 20
PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in PF reads that achieve quality score 30 or higher
PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode.
PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads where PF is defined as passing Illumina's filter.
PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of reads that are PF - pass filter
PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
The number of passing filter reads (PF).
PF_READS - Variable in class picard.illumina.BarcodeMetric
The number of PF reads matching this barcode (always less than or equal to READS).
PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of passing-filter reads assigned to the index.
PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads that were aligned to the reference sequence.
PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
 
PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
 
PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
 
PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
Tracks the number of read pairs that we see that are PF (used to calculate library size)
PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
PF_STATUS - Variable in class picard.sam.ViewSam
 
PF_UNIQUE_READS - Variable in class picard.analysis.directed.PanelMetricsBase
The number of PF_READS that are not marked as duplicates.
PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
This ctor is necessary for when reading metrics from file
PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
 
PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
This ctor is necessary for when reading metrics from file
PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
 
PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
 
pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
The program groups that have been seen during the course of examining the input records.
pgTagArgumentCollection - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
pgTagArgumentCollection - Variable in class picard.sam.MergeBamAlignment
 
PGTagArgumentCollection - Class in picard.sam.util
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
PGTagArgumentCollection() - Constructor for class picard.sam.util.PGTagArgumentCollection
 
PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
 
PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
Median phasing value across all tiles in a lane, applied to the first and second template reads
PHASING_BASE - picard.illumina.parser.IlluminaMetricsCode
 
phasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
 
PhysicalLocation - Interface in picard.sam.util
Small interface that provides access to the physical location information about a cluster.
PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigar(PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
This stores records that are comparable for detecting optical duplicates.
PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
 
PhysicalLocationInt - Class in picard.sam.util
Small class that provides access to the physical location information about a cluster.
PhysicalLocationInt() - Constructor for class picard.sam.util.PhysicalLocationInt
 
PhysicalLocationShort - Class in picard.sam.util
Small class that provides access to the physical location information about a cluster.
PhysicalLocationShort() - Constructor for class picard.sam.util.PhysicalLocationShort
 
picard - package picard
 
picard.analysis - package picard.analysis
 
picard.analysis.artifacts - package picard.analysis.artifacts
 
picard.analysis.directed - package picard.analysis.directed
 
picard.analysis.replicates - package picard.analysis.replicates
 
picard.annotation - package picard.annotation
 
picard.arrays - package picard.arrays
 
picard.arrays.illumina - package picard.arrays.illumina
 
picard.cmdline - package picard.cmdline
 
picard.cmdline.argumentcollections - package picard.cmdline.argumentcollections
 
picard.cmdline.programgroups - package picard.cmdline.programgroups
 
picard.fastq - package picard.fastq
 
picard.filter - package picard.filter
 
picard.fingerprint - package picard.fingerprint
 
picard.illumina - package picard.illumina
 
picard.illumina.parser - package picard.illumina.parser
 
picard.illumina.parser.fakers - package picard.illumina.parser.fakers
 
picard.illumina.parser.readers - package picard.illumina.parser.readers
 
picard.illumina.quality - package picard.illumina.quality
 
picard.metrics - package picard.metrics
 
picard.nio - package picard.nio
 
picard.pedigree - package picard.pedigree
 
picard.reference - package picard.reference
 
picard.sam - package picard.sam
 
picard.sam.markduplicates - package picard.sam.markduplicates
 
picard.sam.markduplicates.util - package picard.sam.markduplicates.util
 
picard.sam.SamErrorMetric - package picard.sam.SamErrorMetric
 
picard.sam.util - package picard.sam.util
 
picard.util - package picard.util
 
picard.util.help - package picard.util.help
 
picard.util.IntervalList - package picard.util.IntervalList
 
picard.vcf - package picard.vcf
 
picard.vcf.filter - package picard.vcf.filter
 
picard.vcf.MendelianViolations - package picard.vcf.MendelianViolations
 
picard.vcf.processor - package picard.vcf.processor
 
picard.vcf.processor.util - package picard.vcf.processor.util
 
PicardCommandLine - Class in picard.cmdline
This is the main class of Picard and is the way of executing individual command line programs.
PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
 
PicardException - Exception in picard
Basic Picard runtime exception that, for now, does nothing much
PicardException(String) - Constructor for exception picard.PicardException
 
PicardException(String, Throwable) - Constructor for exception picard.PicardException
 
PicardHelpDoclet - Class in picard.util.help
Custom Barclay-based Javadoc Doclet used for generating Picard help/documentation.
PicardHelpDoclet() - Constructor for class picard.util.help.PicardHelpDoclet
 
PicardHelpDocWorkUnitHandler - Class in picard.util.help
The Picard Documentation work unit handler class that is the companion to PicardHelpDoclet.
PicardHelpDocWorkUnitHandler(HelpDoclet) - Constructor for class picard.util.help.PicardHelpDocWorkUnitHandler
 
PicardHtsPath - Class in picard.nio
A Subclass of HtsPath with conversion to Path making use of IOUtil
PicardHtsPath(HtsPath) - Constructor for class picard.nio.PicardHtsPath
Create a PicardHtsPath from an existing HtsPath or subclass.
PicardHtsPath(File) - Constructor for class picard.nio.PicardHtsPath
Create a PicardHtsPath from a File reference.
PicardHtsPath(String) - Constructor for class picard.nio.PicardHtsPath
Create a PicardHtsPath from a raw input path string.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
Primary alignment was filtered out.
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
 
pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
 
pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
pickTranscripts(Map<Gene.Transcript, int[]>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
Picks the set of transcripts on which the coverage metrics are to be calculated.
PIPELINE_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version of the pipeline used for this sample
PIPELINE_VERSION - Variable in class picard.arrays.GtcToVcf
 
PIPELINE_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
 
PLATFORM - Variable in class picard.sam.FastqToSam
 
PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
 
PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
 
PLOIDY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
PLUS - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
 
pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible.
pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible.
poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
POLYCLONAL - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
 
POOL_SIZE - Variable in class picard.util.BaitDesigner
 
Pos - picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
 
PosFileFaker - Class in picard.illumina.parser.fakers
Created by jcarey on 3/13/14.
PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
 
PosFileReader - Class in picard.illumina.parser.readers
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
 
Position - picard.illumina.parser.IlluminaDataType
 
POSITION - Variable in class picard.analysis.FingerprintingDetailMetrics
The position of the SNP on the chromosome.
POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
Position within the sequence of the CpG site
PositionBasedDownsampleSam - Class in picard.sam
Summary
PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
 
PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
 
POSITIVE - picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
 
PosParser - Class in picard.illumina.parser
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
 
PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
 
postDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
Returns the PPV defined by the scheme across the subset of call states.
PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
PRE_ADAPTER_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
 
PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
 
PRE_INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
 
PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
 
PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
Performs on-the-fly filtering of the provided VariantContext Iterator such that only variants that satisfy all predicates are emitted.
PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
 
preDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
PREPHASING_BASE - picard.illumina.parser.IlluminaMetricsCode
 
prephasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
 
preprocessIntervalList(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
A function that will be called on an IntervalList prior to splitting it into sub-lists, and is a point where implementations can chose to impose some conditions on the lists, for example, merging overlapping/abutting intervals, removing duplicates, etc.
preprocessIntervalList(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
 
previousReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
 
PRIMARY_MAPPED_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
 
PRIMARY_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
 
PRIMARY_PROPER_PAIR_ONLY - picard.sam.markduplicates.CheckDuplicateMarking.Mode
 
PrimaryAlignmentKey - Class in picard.sam.util
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
PrimaryAlignmentKey(SAMRecord) - Constructor for class picard.sam.util.PrimaryAlignmentKey
 
PrimaryAlignmentSelectionStrategy - Interface in picard.sam
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
When a command does not match any known command, searches for similar commands, using the same method as GIT
PRIOR_ERROR - Static variable in class picard.sam.SamErrorMetric.ErrorMetric
 
PRIOR_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
PROBABILITY - Variable in class picard.sam.DownsampleSam
 
PROBABILITY - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
PROBE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
PROBE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
PROBE_SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Probe sequence not found in reference.
PROBE_SEQUENCE_STRAND_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
PROBE_SET - Variable in class picard.analysis.directed.TargetMetrics
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
PROBE_TERRITORY - Variable in class picard.analysis.directed.TargetMetrics
The number of unique bases covered by the intervals of all probes in the probe set
process() - Method in class picard.vcf.processor.VariantProcessor
 
PROCESS_SINGLE_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
processAllCommandLinePrograms(List<String>, BiConsumer<Class<CommandLineProgram>, CommandLineProgramProperties>) - Static method in class picard.cmdline.PicardCommandLine
Process each CommandLineProgram-derived class given a list of packages.
processDeletionLocus(SamLocusIterator.RecordAndOffset, SamLocusIterator.LocusInfo) - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
Checks if the same record has been seen at the previous locus already, thereby determining whether or not a deletion has already been processed.
processFile() - Method in interface picard.analysis.WgsMetricsProcessor
Method processes the input data and accumulates result data
processFile() - Method in class picard.analysis.WgsMetricsProcessorImpl
Method gets the data from iterator for each locus and processes it with the help of collector.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.BasecallsConverter
Abstract method for processing tiles of data and outputting records for each barcode.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.SortedBasecallsConverter
Set up tile processing and record writing threads for this converter.
processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.UnsortedBasecallsConverter
Set up tile processing and record writing threads for this converter.
product(double...) - Method in class picard.util.MathUtil.LogMath
Computes the sum of the provided log values.
PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
 
PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
 
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
 
PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
PROGRESS_STEP_INTERVAL - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
PROGRESS_STEP_INTERVAL - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
promote(int[]) - Static method in class picard.util.MathUtil
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
PROPER - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
PropertyUtils - Class in picard.util
Utility for loading properties files from resources.
PropertyUtils() - Constructor for class picard.util.PropertyUtils
 
proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
 
PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
 
pSameAlleleWhenMismatchingUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
pSameUmiInIndependentBiDup - Variable in class picard.analysis.replicates.IndependentReplicateMetric
When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance).
PSEUDO_AUTOSOMAL_REGIONS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
 
put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
Store the element in the map with the given key.
PVAL - Variable in class picard.arrays.BafRegressMetrics
The p-value of the estimate

Q

Q_SCORE - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
The (phred) rate of bases that disagree with the reference
Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in all reads that achieve quality score 20 or higher
Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The sum of quality scores of all bases divided by 20
Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The number of bases in all reads that achieve quality score 30 or higher
QdFilter - Class in picard.vcf.filter
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
QdFilter(double) - Constructor for class picard.vcf.filter.QdFilter
 
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
qualities - Variable in class picard.illumina.parser.BclData
 
qualities - Variable in class picard.util.BarcodeEditDistanceQuery
list of quality scores for reads
QUALITY - Variable in class picard.sam.SamToFastq
 
QUALITY_FORMAT - Variable in class picard.sam.FastqToSam
 
QUALITY_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
 
QualityScoreDistribution - Class in picard.analysis
Charts quality score distribution within a BAM file.
QualityScoreDistribution - picard.analysis.CollectMultipleMetrics.Program
 
QualityScoreDistribution() - Constructor for class picard.analysis.QualityScoreDistribution
 
QualityScores - picard.illumina.parser.IlluminaDataType
 
QualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
 
QualityYieldMetricsCollector(boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
 
QuerySortedReadPairIteratorUtil - Class in picard.util
A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
QuerySortedReadPairIteratorUtil() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil
 
QuerySortedReadPairIteratorUtil.ReadPair - Class in picard.util
 
QUIET - Variable in class picard.cmdline.CommandLineProgram
 
QUINTILE_1 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
 
QUINTILE_2 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
 
QUINTILE_3 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
 
QUINTILE_4 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
 
QUINTILE_5 - picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
 

R

R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
R - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
R1R2 - picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
 
RANDOM_SEED - Variable in class picard.sam.DownsampleSam
 
RANDOM_SEED_TAG - Static variable in class picard.sam.DownsampleSam
 
randomSublist(List<T>, int, Random) - Static method in class picard.util.MathUtil
A small utility function to choose n random elements (un-shuffled) from a list
Range - Class in picard.illumina.parser
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
Range(int, int) - Constructor for class picard.illumina.parser.Range
 
rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParser
Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.
RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
The rate of all reads matching this barcode to all reads matching the most prevalent barcode.
RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
 
RawWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
 
rawXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
rawYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
RE_REVERSE - Variable in class picard.sam.SamToFastq
 
read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
Read bytes from the buffer into the supplied array.
READ_CHUNK_SIZE - Variable in class picard.fastq.BamToBfq
 
READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
 
READ_GROUP - picard.analysis.MetricAccumulationLevel
 
READ_GROUP - Variable in class picard.analysis.FingerprintingDetailMetrics
The sequencing read group from which sequence data was fingerprinted.
READ_GROUP - Variable in class picard.analysis.FingerprintingSummaryMetrics
The read group from which sequence data was drawn for comparison.
READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
The read group to which these metrics apply.
READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
 
READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
 
READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The average read length of all the reads (will be fixed for a lane)
READ_LENGTH - Variable in class picard.analysis.CollectWgsMetrics
 
READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
 
READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
READ_NAME_PREFIX - Variable in class picard.fastq.BamToBfq
 
READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
READ_NAME_REGEX - Variable in class picard.sam.PositionBasedDownsampleSam
 
READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
 
READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of read pairs that were marked as duplicates.
READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of read pairs duplicates that were caused by optical duplication.
READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
The total number of read pairs that were examined in the entire distribution.
READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
The number of mapped read pairs examined.
READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
The number of reads whose start position is at the start of a window of this GC.
READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
 
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
 
READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
READ_STRUCTURE - Variable in class picard.illumina.ExtractBarcodesProgram
 
READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
 
READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
 
read1 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
 
READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
 
READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
 
READ1_TRIM - Variable in class picard.sam.SamToFastq
 
read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
 
read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
 
read2 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
 
READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
 
READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
 
READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
 
READ2_TRIM - Variable in class picard.sam.SamToFastq
 
read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
 
read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
 
ReadBaseStratification - Class in picard.sam.SamErrorMetric
Classes, methods, and enums that deal with the stratification of read bases and reference information.
ReadBaseStratification() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification
 
ReadBaseStratification.BinnedReadCycleStratifier - Class in picard.sam.SamErrorMetric
Stratifies into quintiles of read cycle.
ReadBaseStratification.CigarOperatorsInReadStratifier - Class in picard.sam.SamErrorMetric
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
ReadBaseStratification.CollectionStratifier - Class in picard.sam.SamErrorMetric
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
ReadBaseStratification.Consensus - Enum in picard.sam.SamErrorMetric
Types of consensus reads as determined by the number of duplicates used from first and second strands.
ReadBaseStratification.ConsensusStratifier - Class in picard.sam.SamErrorMetric
Stratify by tags used during duplex and single index consensus calling.
ReadBaseStratification.CycleBin - Enum in picard.sam.SamErrorMetric
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
ReadBaseStratification.FlowCellTileStratifier - Class in picard.sam.SamErrorMetric
Stratifies base into their read's tile which is parsed from the read-name.
ReadBaseStratification.FlowCellXStratifier - Class in picard.sam.SamErrorMetric
Stratifies base into their read's X coordinate which is parsed from the read-name.
ReadBaseStratification.FlowCellYStratifier - Class in picard.sam.SamErrorMetric
Stratifies base into their read's Y coordinate which is parsed from the read-name.
ReadBaseStratification.GCContentStratifier - Class in picard.sam.SamErrorMetric
A stratifier that uses GC (of the read) to stratify.
ReadBaseStratification.IndelLengthStratifier - Class in picard.sam.SamErrorMetric
Stratifies according to the length of an insertion or deletion.
ReadBaseStratification.IndelsInReadStratifier - Class in picard.sam.SamErrorMetric
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
ReadBaseStratification.LongShortHomopolymer - Enum in picard.sam.SamErrorMetric
 
ReadBaseStratification.LongShortHomopolymerStratifier - Class in picard.sam.SamErrorMetric
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
ReadBaseStratification.MismatchesInReadStratifier - Class in picard.sam.SamErrorMetric
Stratifies according to the overall mismatches (from SAMTag.NM) that the read has against the reference, NOT including the current base.
ReadBaseStratification.NsInReadStratifier - Class in picard.sam.SamErrorMetric
Stratify by the number of Ns found in the read.
ReadBaseStratification.PairOrientation - Enum in picard.sam.SamErrorMetric
An enum for holding a reads read-pair's Orientation (i.e.
ReadBaseStratification.PairStratifier<T extends Comparable<T>,​R extends Comparable<R>> - Class in picard.sam.SamErrorMetric
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
ReadBaseStratification.ProperPaired - Enum in picard.sam.SamErrorMetric
An enum to hold information about the "properness" of a read pair
ReadBaseStratification.ReadDirection - Enum in picard.sam.SamErrorMetric
An enum for holding the direction for a read (positive strand or negative strand
ReadBaseStratification.ReadOrdinality - Enum in picard.sam.SamErrorMetric
An enum to hold the ordinality of a read
ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>> - Interface in picard.sam.SamErrorMetric
The main interface for a stratifier.
ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
Heart of CLP.
readCount - Variable in class picard.analysis.directed.TargetMetricsCollector.Coverage
 
ReadData - Class in picard.illumina.parser
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
ReadData() - Constructor for class picard.illumina.parser.ReadData
 
ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
 
ReadDataManipulationProgramGroup - Class in picard.cmdline.programgroups
Tools that manipulate read data in SAM, BAM or CRAM format
ReadDataManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
 
ReadDescriptor - Class in picard.illumina.parser
Represents one set of cycles in an ReadStructure (e.g.
ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
 
readDirectionStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into their read's Direction (i.e.
ReadEnds - Class in picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
 
ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesWithBarcodes - Class in picard.sam.markduplicates.util
 
ReadEndsForMarkDuplicatesWithBarcodes() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
ReadEndsForMarkDuplicatesWithBarcodesCodec - Class in picard.sam.markduplicates.util
Created by nhomer on 9/13/15.
ReadEndsForMarkDuplicatesWithBarcodesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
 
ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
A class to store individual records for MarkDuplicatesWithMateCigar.
ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
Builds a read ends object that represents a single read.
ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
Creates a shallow copy from the "other"
readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
 
READGROUP - picard.fingerprint.CrosscheckMetric.DataType
 
READGROUP_ID_REGEX - Static variable in class picard.sam.AddOrReplaceReadGroups
 
readgroupStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies to the readgroup id of the read.
readHeader(int) - Method in class picard.illumina.parser.readers.CbclReader
Reads the Cbcl header and sets up the data streams.
readIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
 
readLaneTiles(File, ReadStructure, ValidationStringency, int) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
readLengths - Variable in class picard.illumina.parser.ReadStructure
 
ReadNameEncoder - Interface in picard.fastq
 
ReadNameParser - Class in picard.sam.util
Provides access to the physical location information about a cluster.
ReadNameParser() - Constructor for class picard.sam.util.ReadNameParser
Creates are read name parser using the default read name regex and optical duplicate distance.
ReadNameParser(String) - Constructor for class picard.sam.util.ReadNameParser
Creates are read name parser using the given read name regex.
ReadNameParser(String, Log) - Constructor for class picard.sam.util.ReadNameParser
Creates are read name parser using the given read name regex.
readNameRegex - Variable in class picard.sam.util.ReadNameParser
 
readNextLine() - Method in class picard.util.AbstractInputParser
 
readNextLine() - Method in class picard.util.BasicInputParser
Workhorse method that reads the next line from the underlying reader
readOneBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
readOrdinalityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into their read's Ordinality (i.e.
readOrientationStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into their read-pair's Orientation (i.e.
ReadPair() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
 
readPairednessStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies bases into their read's Proper-pairedness
READS - Variable in class picard.illumina.BarcodeMetric
The total number of reads matching the barcode.
READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The total number of reads examined
READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
Number of mapped reads processed
READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of aligned reads whose mate pair was also aligned to the reference.
READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded for exceeding the mismatch threshold
READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded due to being too short
READS_TO_ALIGN - Variable in class picard.fastq.BamToBfq
 
READS_USED - Variable in class picard.analysis.GcBiasDetailMetrics
This option is used to mark including or excluding duplicates.
READS_USED - Variable in class picard.analysis.GcBiasSummaryMetrics
This option is used to mark including or excluding duplicates.
READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
Number of reads discarded for having no CpG sites
ReadStructure - Class in picard.illumina.parser
Describes the intended logical output structure of clusters of an Illumina run.
ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
Converts readStructureString into a List and calls the primary constructor using this List as it's argument.
ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
ReadStructure.Substructure - Class in picard.illumina.parser
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
readSubsequence - Variable in class picard.util.BarcodeEditDistanceQuery
list of barcode reads
readTwoBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
 
ReadType - Enum in picard.illumina.parser
A read type describes a stretch of cycles in an ReadStructure (e.g.
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingAdapterFilter
 
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingDuplicateFilter
 
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingFilter
Return true if we are to filter this record out, false otherwise.
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingMapQFilter
 
reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingPairedFilter
 
Record(int, int, Float, Float, float, IlluminaGenotype) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
 
RECORDS_ONLY - Variable in class picard.sam.ViewSam
 
RECOVER_SWAPPED_REF_ALT - Variable in class picard.vcf.LiftoverVcf
 
RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
The red intensity value for the control.
ref() - Method in enum picard.analysis.artifacts.Transition
Gets the reference for the transition.
REF_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
The reference base (or it's complement).
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The (upper-case) original base on the reference strand.
REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The (upper-case) original base on the reference strand.
REF_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
The number of reference bases observed.
REF_FLAT - Variable in class picard.analysis.CollectMultipleMetrics
 
REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
 
REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as C in read 1 and G in read 2.
REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The number of reference alleles observed as G in read 1 and C in read 2.
REF_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of reference alleles observed
REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
 
REFERENCE - Variable in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
 
REFERENCE - Variable in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
 
REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
 
REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
 
REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
 
REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
 
REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
ReferenceArgumentCollection - Interface in picard.cmdline.argumentcollections
Base interface for a reference argument collection.
referenceBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
 
ReferenceProgramGroup - Class in picard.cmdline.programgroups
Tools that analyze and manipulate FASTA format references
ReferenceProgramGroup() - Constructor for class picard.cmdline.programgroups.ReferenceProgramGroup
 
referenceSequence - Variable in class picard.cmdline.CommandLineProgram
 
RefFlatReader - Class in picard.annotation
Loads gene annotations from a refFlat file into an OverlapDetector.
RefFlatReader.RefFlatColumns - Enum in picard.annotation
 
ReflectionUtil - Class in picard.util
Class which contains utility functions that use reflection.
ReflectionUtil() - Constructor for class picard.util.ReflectionUtil
 
reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
REJECT - Variable in class picard.util.LiftOverIntervalList
 
REJECT - Variable in class picard.vcf.LiftoverVcf
 
remove() - Method in class picard.illumina.parser.MultiTileParser
 
remove() - Method in class picard.illumina.parser.PerTileParser
 
remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
 
remove() - Method in class picard.illumina.parser.readers.BclReader
 
remove() - Method in class picard.illumina.parser.readers.FilterFileReader
 
remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
 
remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
 
remove() - Method in class picard.util.AsyncIterator
 
remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
 
remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
 
remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
 
remove() - Method in class picard.vcf.PairedVariantSubContextIterator
 
remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
 
remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
remove(int, String) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
 
remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
Remove element with given key from the map.
remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Removes the end from this set, if present
REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
 
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
 
REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
 
REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
 
REMOVE_SEQUENCING_DUPLICATES - Variable in class picard.sam.markduplicates.MarkDuplicates
 
removeIncompleteTrios() - Method in class picard.pedigree.PedFile
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
RenameSampleInVcf - Class in picard.vcf
Renames a sample within a VCF or BCF.
RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
 
renderPhasingMetricsFilesFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
 
REORDER_INPUT_BY_FIRST_VARIANT - Variable in class picard.vcf.GatherVcfs
 
ReorderSam - Class in picard.sam
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
ReorderSam() - Constructor for class picard.sam.ReorderSam
 
REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
 
replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
Replaces a given end with the other end.
ReplaceSamHeader - Class in picard.sam
 
ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
 
replicationRateFromReplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
An estimate of the duplication rate that is based on the duplicate sets we observed.
REPORT_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
REPORTED_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The sex, as reported by the collaborator
RepresentativeReadIndexer - Class in picard.sam.util
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
RepresentativeReadIndexer() - Constructor for class picard.sam.util.RepresentativeReadIndexer
 
RepresentativeReadIndexerCodec - Class in picard.sam.markduplicates.util
Codec for read names and integers that outputs the primitive fields and reads them back.
RepresentativeReadIndexerCodec() - Constructor for class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
representativeReadIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
 
REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
 
RequiredOutputArgumentCollection - Class in picard.cmdline.argumentcollections
 
RequiredOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
 
RequiredOutputArgumentCollection(File) - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
 
RequiredReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
Argument collection for references that are required (and not common).
RequiredReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
 
requiresReference() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
requiresReference() - Method in class picard.analysis.CollectOxoGMetrics
 
requiresReference() - Method in class picard.analysis.CollectWgsMetrics
 
requiresReference() - Method in class picard.arrays.GtcToVcf
 
requiresReference() - Method in class picard.cmdline.CommandLineProgram
 
requiresReference() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
 
requiresReference() - Method in class picard.fingerprint.ExtractFingerprint
 
requiresReference() - Method in class picard.fingerprint.IdentifyContaminant
 
requiresReference() - Method in class picard.reference.ExtractSequences
 
requiresReference() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
requiresReference() - Method in class picard.sam.MergeBamAlignment
 
requiresReference() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
requiresReference() - Method in class picard.sam.SetNmMdAndUqTags
 
requiresReference() - Method in class picard.util.BaitDesigner
 
resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
 
RESTORE_HARDCLIPS - Variable in class picard.sam.RevertSam
 
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
 
result() - Method in class picard.vcf.CallingMetricAccumulator
 
result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
 
RESULT - Variable in class picard.fingerprint.CrosscheckMetric
 
REV_COMPED_ALLELES - Static variable in class picard.util.LiftoverUtils
 
REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
reverseComplementVariantContext(VariantContext, Interval, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
 
RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum in picard.sam
Used as a return for the canSkipSAMFile function.
RevertSam - Class in picard.sam
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
RevertSam() - Constructor for class picard.sam.RevertSam
 
RevertSam.FileType - Enum in picard.sam
 
revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.
RExecutor - Class in picard.util
Util class for executing R scripts.
RExecutor() - Constructor for class picard.util.RExecutor
 
RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
RG_TAG - Variable in class picard.sam.SamToFastq
 
RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGFO - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGID - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGKS - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
 
RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
 
RIBOSOMAL - picard.annotation.LocusFunction
 
RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary alignments that align to ribosomal sequence.
RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
 
ribosomalInitialValue - Variable in class picard.analysis.directed.RnaSeqMetricsCollector
 
RIGHT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_FILE - Variable in class picard.sam.SamComparisonMetric
Right file used in comparison
RIGHT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
 
RIGHT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
 
RIGHT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
 
rightVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
 
RIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
RnaSeqMetrics - Class in picard.analysis
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
RnaSeqMetrics - picard.analysis.CollectMultipleMetrics.Program
 
RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
 
RnaSeqMetricsCollector - Class in picard.analysis.directed
 
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
 
RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean, int) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
 
RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector - Class in picard.analysis.directed
 
RnaSeqMetricsCollector.StrandSpecificity - Enum in picard.analysis.directed
 
round(double...) - Static method in class picard.util.MathUtil
returns a long array containing the rounded values of the input array
round(double, int) - Static method in class picard.util.MathUtil
Round off the value to the specified precision.
RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
 
RrbsCpgDetailMetrics - Class in picard.analysis
Holds information about CpG sites encountered for RRBS processing QC
RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
 
RrbsMetricsCollector - Class in picard.analysis
 
RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
 
RrbsSummaryMetrics - Class in picard.analysis
Holds summary statistics from RRBS processing QC
RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
 
RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
 
RS_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
rsNames - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
rsNameToIndex - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
run() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
run method which extracts barcodes and accumulates metrics for an entire tile
run() - Method in class picard.Test
 
RUN_BARCODE - Variable in class picard.fastq.BamToBfq
 
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
 
RUN_DATE - Variable in class picard.sam.FastqToSam
 
RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
 
RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam
 

S

S - picard.illumina.parser.ReadType
 
S_LOCS_FILE - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
 
sam - picard.sam.RevertSam.FileType
 
SAM_FILES - Variable in class picard.sam.CompareSAMs
 
SamAlignmentMerger - Class in picard.sam
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int) - Constructor for class picard.sam.SamAlignmentMerger
Constructor with a default value for unmappingReadStrategy
SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int, AbstractAlignmentMerger.UnmappingReadStrategy, List<String>) - Constructor for class picard.sam.SamAlignmentMerger
Constructor
SamComparison - Class in picard.sam.util
Compare two SAM/BAM files.
SamComparison(SamReader, SamReader) - Constructor for class picard.sam.util.SamComparison
Note: the caller must make sure the SamReaders are closed properly.
SamComparison(SamReader, SamReader, String, String, SAMComparisonArgumentCollection) - Constructor for class picard.sam.util.SamComparison
 
SamComparison.AlignmentComparison - Enum in picard.sam.util
 
samComparisonArgumentCollection - Variable in class picard.sam.CompareSAMs
 
SAMComparisonArgumentCollection - Class in picard.sam.util
Argument collection for SAM comparison
SAMComparisonArgumentCollection() - Constructor for class picard.sam.util.SAMComparisonArgumentCollection
 
SamComparisonMetric - Class in picard.sam
Metric for results of SamComparison.
SamComparisonMetric() - Constructor for class picard.sam.SamComparisonMetric
 
SamFormatConverter - Class in picard.sam
Converts a BAM file to human-readable SAM output or vice versa
SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
 
SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
 
SAMPLE - picard.analysis.MetricAccumulationLevel
 
SAMPLE - picard.fingerprint.CrosscheckMetric.DataType
 
SAMPLE - Variable in class picard.analysis.FingerprintingDetailMetrics
The name of the sample who's genotypes the sequence data was compared to.
SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
The sample whose known genotypes the sequence data was compared to.
SAMPLE - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
SAMPLE - Variable in class picard.arrays.BafRegressMetrics
The sample name
SAMPLE - Variable in class picard.metrics.MultilevelMetrics
The sample to which these metrics apply.
SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
 
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
 
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The name of the sample being assayed.
SAMPLE_ALIAS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the sample
SAMPLE_ALIAS - Variable in class picard.arrays.GtcToVcf
 
SAMPLE_ALIAS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
SAMPLE_ALIAS - Variable in class picard.fingerprint.ExtractFingerprint
 
SAMPLE_ALIAS - Variable in class picard.fingerprint.FingerprintMetrics
The Sample alias taken from RG header or #CHROME line
SAMPLE_ALIAS - Variable in class picard.fingerprint.IdentifyContaminant
 
SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
 
SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
 
SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
The name of the sample being assayed
SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SAMPLE_INDIVIDUAL_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
 
SAMPLE_NAME - Variable in class picard.sam.FastqToSam
 
SAMPLE_SIZE - Variable in class picard.analysis.CollectWgsMetrics
 
SAMPLE_SIZE - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
SAMPLE_SIZE - Variable in class picard.analysis.TheoreticalSensitivityMetrics
Number of samples drawn at each depth in the depth distribution.
sampleBarcodes - Variable in class picard.illumina.parser.ReadStructure
 
sampleCumulativeSums(int, int, boolean) - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
 
SAMPLES_FILE - Variable in class picard.arrays.VcfToAdpc
 
SAMRecordAndReference - Class in picard.metrics
 
SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
 
SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable> - Class in picard.metrics
 
SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
 
SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,​HKEY extends Comparable> - Class in picard.metrics
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
 
samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
This class sets the duplicate read flag as the result state when examining sets of records.
SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
SamSequenceRecordsIterator(File, boolean) - Constructor for class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
SamToBfqWriter - Class in picard.fastq
Class to take unmapped reads in SAM/BAM/CRAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
SamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.SamToBfqWriter
Constructor
SamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.SamToBfqWriter
Constructor
SamToFastq - Class in picard.sam
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
SamToFastq() - Constructor for class picard.sam.SamToFastq
 
SamToFastqWithTags - Class in picard.sam
Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
SamToFastqWithTags() - Constructor for class picard.sam.SamToFastqWithTags
 
SANITIZE - Variable in class picard.sam.RevertSam
 
scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor.
SCAN_WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
 
scanDir(File, String) - Method in class picard.cmdline.ClassFinder
Scans a directory on the filesystem for classes.
scanJar(File, String) - Method in class picard.cmdline.ClassFinder
Scans the entries in a ZIP/JAR file for classes under the parent package.
SCANNER_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The name of the scanner used for this sample
SCANNER_NAME - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
scatter(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
Scatter an IntervalList into several IntervalLists.
SCATTER_CONTENT - Variable in class picard.util.IntervalListTools
 
SCATTER_COUNT - Variable in class picard.util.IntervalListTools
 
ScatterIntervalsByNReferenceArgumentCollection() - Constructor for class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
 
ScatterIntervalsByNs - Class in picard.util
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
 
ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection - Class in picard.util
 
scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
The underlying scheme
score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
SCORE - Variable in class picard.util.IntervalListToBed
 
SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation of clusters per tile.
SD_COVERAGE - Variable in class picard.analysis.WgsMetrics
The standard deviation of coverage of the genome after all filters are applied.
SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation in percentage of pf clusters per tile.
SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
The standard deviation in number of pf clusters per tile.
SD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
The standard deviation of the read lengths.
SECOND - picard.illumina.parser.TileTemplateRead
 
SECOND - picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
 
SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
 
SECOND_INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
 
SECOND_INPUT - Variable in class picard.util.IntervalListTools
 
SECOND_INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
 
SECOND_OF_PAIR - picard.analysis.AlignmentSummaryMetrics.Category
 
SECOND_READ_TRANSCRIPTION_STRAND - picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
 
SECONDARY_OR_SUPPLEMENTARY_RDS - Variable in class picard.sam.DuplicationMetrics
The number of reads that were either secondary or supplementary
seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
 
seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
 
seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
 
sensitivityAtConstantDepth(int, Histogram<Integer>, double, int, double, long) - Static method in class picard.analysis.TheoreticalSensitivity
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant depth.
seq(double, double, double) - Static method in class picard.util.MathUtil
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
SEQUENCE_DICTIONARY - Variable in class picard.annotation.SortGff
 
SEQUENCE_DICTIONARY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
 
SEQUENCE_DICTIONARY - Variable in class picard.fingerprint.LiftOverHaplotypeMap
 
SEQUENCE_DICTIONARY - Variable in class picard.sam.ReorderSam
 
SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
 
SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
 
SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
 
SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
Sequence the CpG is seen in
SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
 
SEQUENCE_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
 
SequenceDictionaryUtils - Class in picard.util
Class with helper methods for generating and writing SequenceDictionary objects.
SequenceDictionaryUtils() - Constructor for class picard.util.SequenceDictionaryUtils
 
SequenceDictionaryUtils.SamSequenceRecordsIterator - Class in picard.util
 
SEQUENCING - picard.sam.markduplicates.MarkDuplicates.DuplicateType
 
SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
 
SequencingArtifactMetrics - Class in picard.analysis.artifacts
 
SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
 
SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
Bait bias artifacts broken down by context.
SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
Pre-adapter artifacts broken down by context.
SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
Summary analysis of a single pre-adapter artifact.
SET_ONLY_UQ - Variable in class picard.sam.SetNmMdAndUqTags
 
setAddPGTagToReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
Set addPGTagToReads.
setAllowDuplicateReads(boolean) - Method in class picard.fingerprint.FingerprintChecker
Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
setAssayFormat(String) - Method in class picard.arrays.illumina.IlluminaManifest
 
setAttributesToReverse(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
Sets the set of attributes to be reversed on reads marked as negative strand.
setAttributesToReverseComplement(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
Sets the set of attributes to be reverse complemented on reads marked as negative strand.
setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the name of the bait set explicitly instead of inferring it from the bait file.
setBases(byte[]) - Method in class picard.illumina.parser.ReadData
 
setBigDuplicateSetSize(int) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
Sets the size of a set that is big enough to log progress about.
setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
 
setConverter(BasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.BasecallsConverter
Must be called before doTileProcessing.
setCounter(long) - Method in class picard.analysis.AbstractWgsMetricsCollector
Sets the counter to the current number of processed loci.
setDateManufactured(String) - Method in class picard.arrays.illumina.IlluminaManifest
 
setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
 
setDefaultSampleID(String) - Method in class picard.fingerprint.FingerprintChecker
 
setDescriptorFileName(String) - Method in class picard.arrays.illumina.IlluminaManifest
 
setDupe(boolean) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
setGcCacheSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
 
setGenomeAssembly(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
setGenotypingErrorRate(double) - Method in class picard.fingerprint.FingerprintChecker
Sets the assumed genotyping error rate used when accurate error rates are not available.
setHardClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
 
setHgGenomeBuild(String) - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
setIdentifier(String) - Method in class picard.arrays.illumina.InfiniumDataFile
 
setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
 
setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
setLane(int) - Method in class picard.illumina.parser.ClusterData
 
setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setLibraryId(short) - Method in interface picard.sam.util.PhysicalLocation
 
setLibraryId(short) - Method in class picard.sam.util.PhysicalLocationInt
 
setLocationBinSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
defaults to 2500
setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
 
setLociCount(int) - Method in class picard.arrays.illumina.IlluminaManifest
 
setLocusMaxReads(int) - Method in class picard.fingerprint.FingerprintChecker
 
setLongHomopolymer(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
defaults to 6
setManifestFileParser(CsvInputParser) - Method in class picard.arrays.illumina.IlluminaManifest
 
setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
 
setMaxDuplicateSetSize(long) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
Sets the size of a set that is too big to process.
setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
 
setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
Allows the caller to override the maximum records in RAM.
setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
 
setMinimumBaseQuality(int) - Method in class picard.fingerprint.FingerprintChecker
Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
setMinimumMappingQuality(int) - Method in class picard.fingerprint.FingerprintChecker
Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
 
setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
 
setNearProbeDistance(int) - Method in class picard.analysis.directed.TargetMetricsCollector
Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
SetNmAndUqTags - Class in picard.sam
Deprecated.
SetNmAndUqTags() - Constructor for class picard.sam.SetNmAndUqTags
Deprecated.
 
SetNmMdAndUqTags - Class in picard.sam
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
SetNmMdAndUqTags() - Constructor for class picard.sam.SetNmMdAndUqTags
 
setNoSideEffects(boolean) - Method in class picard.analysis.directed.TargetMetricsCollector
In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases.
setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
setNumAssays(int) - Method in class picard.arrays.illumina.IlluminaManifest
 
setOffset(int) - Method in class picard.arrays.illumina.InfiniumFileTOC
 
setOffsetX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setOffsetY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
Either set this value if not already set, or if already set, throw an exception if new value != current value.
setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
 
setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
 
setPerBaseOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the (optional) File to write per-base coverage information to.
setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
Sets the (optional) File to write per-target coverage information to.
setPf(boolean) - Method in class picard.illumina.parser.ClusterData
 
setpLossofHet(double) - Method in class picard.fingerprint.FingerprintChecker
 
setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo) - Method in class picard.illumina.parser.CbclData
 
setPriorError(double) - Static method in class picard.sam.SamErrorMetric.ErrorMetric
 
setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.
setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
 
setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
 
setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
 
setReadGroup(short) - Method in interface picard.sam.util.PhysicalLocation
 
setReadGroup(short) - Method in class picard.sam.util.PhysicalLocationInt
 
setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
 
setReferenceFasta(File) - Method in class picard.fingerprint.FingerprintChecker
 
setReferenceSequence(File) - Method in class picard.analysis.SinglePassSamProgram
Set the reference File.
setReserved1(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setReserved2(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setReserved3(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setReserved4(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setReserved5(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setReserved6(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
 
setRsId(String) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
 
setScaleX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setScaleY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setShear(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setSize - Variable in class picard.sam.util.RepresentativeReadIndexer
 
setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
 
setSpecies(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
setTheta(float) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
When this number of adapters have been matched, discard the least-frequently matching ones.
setTile(int) - Method in class picard.illumina.parser.ClusterData
 
setTile(short) - Method in interface picard.sam.util.PhysicalLocation
 
setTile(short) - Method in class picard.sam.util.PhysicalLocationInt
 
setTileLimits(Integer, Integer) - Method in class picard.illumina.BasecallsConverter
Uses the firstTile and tileLimit parameters to set which tiles will be processed.
setTiles(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
 
setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
 
setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
 
setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
 
setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectQualityYieldMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
 
setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
 
setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
 
setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.
setup(SAMFileHeader, File) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
setup(VCFHeader) - Method in class picard.vcf.CallingMetricAccumulator
 
setup(VCFHeader) - Method in class picard.vcf.GvcfMetricAccumulator
 
setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
 
setUri(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
 
setValidationStringency(ValidationStringency) - Method in class picard.fingerprint.FingerprintChecker
 
setValuesFromAlignment(SAMRecord, SAMRecord, boolean) - Method in class picard.sam.AbstractAlignmentMerger
Sets the values from the alignment record on the unaligned BAM record.
setVersion(int) - Method in class picard.arrays.illumina.InfiniumTransformation
 
setWordCount(int) - Method in class picard.util.AbstractInputParser
 
setX(int) - Method in class picard.illumina.parser.ClusterData
 
setX(int) - Method in interface picard.sam.util.PhysicalLocation
 
setX(int) - Method in class picard.sam.util.PhysicalLocationInt
 
setX(int) - Method in class picard.sam.util.PhysicalLocationShort
 
setY(int) - Method in class picard.illumina.parser.ClusterData
 
setY(int) - Method in interface picard.sam.util.PhysicalLocation
 
setY(int) - Method in class picard.sam.util.PhysicalLocationInt
 
setY(int) - Method in class picard.sam.util.PhysicalLocationShort
 
Sex - Enum in picard.pedigree
Represents the sex of an individual.
shiftedLogEvidenceProbability() - Method in class picard.fingerprint.HaplotypeProbabilities
Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
returns the log-probability the evidence, using as priors the posteriors of another object
shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
 
SHORT_HOMOPOLYMER - picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
 
shortToByteArray(short) - Static method in class picard.arrays.illumina.InfiniumDataFile
Utility method to convert a short to a byte array
shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
Returns true if we should track this for optical duplicate detection, false otherwise
shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
 
shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
 
Simple - picard.util.BaitDesigner.DesignStrategy
Ultra simple bait design algorithm that just lays down baits starting at the target start position until either the bait start runs off the end of the target or the bait would run off the sequence
SimpleErrorCalculator - Class in picard.sam.SamErrorMetric
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
SimpleErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.SimpleErrorCalculator
 
SimpleMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
SimpleMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
 
SIMPLEX_CONSENSUS - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Read which had multiple observations, but all from the same strand (or the strand could not be determined).
SIMPLEX_SINGLETON - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Read which only one observation is made.
SINGLE_END - picard.util.IlluminaUtil.IlluminaAdapterPair
 
SingleBarcodeDistanceMetric - Class in picard.util
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
SingleBarcodeDistanceMetric(byte[], byte[], byte[], int, int) - Constructor for class picard.util.SingleBarcodeDistanceMetric
 
SinglePassSamProgram - Class in picard.analysis
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
 
size() - Method in class picard.fingerprint.HaplotypeBlock
Returns the number of SNPs within the haplotype block.
size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
size() - Method in class picard.sam.markduplicates.util.MarkQueue
The number of records currently in this queue.
size() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
 
size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
The number of records in this set
size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
 
SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
 
sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
 
sizeInRam() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
 
sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
 
Skip - Static variable in enum picard.illumina.parser.ReadType
 
SKIP_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
SKIP_MATE_VALIDATION - Variable in class picard.sam.ValidateSamFile
 
skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
 
skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
 
skips - Variable in class picard.illumina.parser.ReadStructure
 
Snp - Class in picard.fingerprint
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
Snp(String, String, int, byte, byte, double, List<String>) - Constructor for class picard.fingerprint.Snp
 
SNP - picard.util.VariantType
 
SNP - Variable in class picard.analysis.FingerprintingDetailMetrics
The name of a representative SNP within the haplotype that was compared.
SNP_ALLELES - Variable in class picard.analysis.FingerprintingDetailMetrics
The possible alleles for the SNP.
SNP_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
 
SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
snpCounter - Variable in class picard.vcf.GenotypeConcordance
 
snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
 
softClipsLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
SORT - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
SORT - Variable in class picard.illumina.IlluminaBasecallsToSam
 
SORT - Variable in class picard.util.BedToIntervalList
 
SORT - Variable in class picard.util.IntervalListToBed
 
SORT - Variable in class picard.util.IntervalListTools
 
SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
 
SORT_ORDER - Variable in class picard.sam.FastqToSam
 
SORT_ORDER - Variable in class picard.sam.FilterSamReads
 
SORT_ORDER - Variable in class picard.sam.FixMateInformation
 
SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
 
SORT_ORDER - Variable in class picard.sam.MergeSamFiles
 
SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
 
SORT_ORDER - Variable in class picard.sam.RevertSam
 
SORT_ORDER - Variable in class picard.sam.SortSam
 
SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
SortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.SortedBasecallsConverter
Constructs a new SortedBaseCallsConverter.
SortGff - Class in picard.annotation
Summary
SortGff() - Constructor for class picard.annotation.SortGff
 
SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
 
SortSam - Class in picard.sam
Sorts a SAM or BAM file.
SortSam() - Constructor for class picard.sam.SortSam
 
SortVcf - Class in picard.vcf
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
SortVcf() - Constructor for class picard.vcf.SortVcf
 
SOURCE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
SOURCE - Variable in class picard.fingerprint.FingerprintMetrics
The originating file (if available) for this fingerprint
SOURCE_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
SOURCE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
SOURCE_SEQUENCE_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Source sequence is invalid (contains invalid character).
SOURCE_SEQUENCE_MISMATCH - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
SOURCE_SEQUENCE_STRAND_INVALID - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Deprecated.
- but used in existing extended manifest files.
SOURCE_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
SOURCE_VERSION_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
specialArgumentsCollection - Variable in class picard.cmdline.CommandLineProgram
 
SPECIES - Variable in class picard.sam.CreateSequenceDictionary
 
SPECIES_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
split(String, String[], String) - Method in class picard.Test
 
SPLIT_TO_N_FILES - Variable in class picard.sam.SplitSamByNumberOfReads
 
SPLIT_TO_N_READS - Variable in class picard.sam.SplitSamByNumberOfReads
 
SplitSamByLibrary - Class in picard.sam
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
 
SplitSamByNumberOfReads - Class in picard.sam
Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
SplitSamByNumberOfReads() - Constructor for class picard.sam.SplitSamByNumberOfReads
 
SplitVcfs - Class in picard.vcf
Splits the input VCF file into two, one for indels and one for SNPs.
SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
 
STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
Standard deviation of insert sizes over the "core" of the distribution.
StandardOptionDefinitions - Class in picard.cmdline
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
 
start - Variable in class picard.annotation.Gene.Transcript.Exon
 
start - Variable in class picard.illumina.parser.Range
 
start() - Method in class picard.annotation.Gene.Transcript
 
start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
 
start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
Starts the work of the executor, returning immediately.
start() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
start() - Method in class picard.vcf.processor.VcfPathSegment
 
start(RootDoc) - Static method in class picard.util.help.PicardHelpDoclet
Create a doclet of the appropriate type and generate the FreeMarker templates properties.
stddev(double[], double) - Static method in class picard.util.MathUtil
Calculated the standard deviation of an array of doubles.
stddev(double[], int, int) - Static method in class picard.util.MathUtil
Calculated the standard deviation of an array of doubles.
stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
Calculated the standard deviation of an array of doubles.
STDERR - Variable in class picard.arrays.BafRegressMetrics
The standard error of the estimate
stop() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
stop() - Method in class picard.vcf.processor.VcfPathSegment
 
STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
 
STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
 
STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
 
STOP_AFTER - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
 
STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
 
STRAND - picard.annotation.RefFlatReader.RefFlatColumns
 
STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
 
STRATEGY - Variable in class picard.sam.DownsampleSam
 
STRATIFIER_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
 
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
Returns the number of bases associated with I and D CIGAR elements.
stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
 
stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
 
STRICT - Variable in class picard.vcf.SplitVcfs
 
stringSeqsToString(String[], String) - Static method in class picard.util.IlluminaUtil
 
STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
Deprecated.
SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
 
subsetAlleles(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
Create the new GenotypesContext with the subsetted PLs and ADs Expects allelesToKeep to be in the same order in which they are in originalAlleles.
subsetAlleles(VariantContext, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
 
subsettedPLIndices(List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e.
subsetVCToMatchSnp(VariantContext, Snp) - Static method in class picard.util.AlleleSubsettingUtils
Method to subset the alleles in the VariantContext to those in the input snp.
SUBSTITUTION - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
SUBSTITUTION_RATE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
The rate of the substitution in question.
Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
SUBTRACT - picard.util.IntervalListTools.Action
 
subtractMax(double[]) - Static method in class picard.util.MathUtil
 
sum(double...) - Method in class picard.util.MathUtil.LogMath
Computes the sum of the provided log values.
sum(double[]) - Static method in class picard.util.MathUtil
Returns the sum of the elements in the array.
sum(double[], double) - Static method in class picard.util.MathUtil
calculates the sum of an array and a double.
sum(double[], double[]) - Static method in class picard.util.MathUtil
calculates the sum of the arrays as a third array.
sum(long[], int, int) - Static method in class picard.util.MathUtil
Returns the sum of the elements in the array starting with start and ending before stop.
SUMMARY - picard.sam.ValidateSamFile.Mode
 
SUMMARY - Variable in class picard.metrics.GcBiasMetrics
 
SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
 
SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
 
SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
 
SUMMARY_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
 
summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
 
SUPPORTED_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
SUPPORTED_CHAIN_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
SUPPORTED_REFERENCE_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
 
supportedTypes() - Method in class picard.illumina.parser.PosParser
 
supportsMetricAccumulationLevel() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
 
swapAlleles(VariantContext, Allele, Allele) - Static method in class picard.util.AlleleSubsettingUtils
Swaps one of the alleles in a VC (and its genotypes) with another.
SWAPPED_ALLELES - Static variable in class picard.util.LiftoverUtils
Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
swapRefAlt(VariantContext, Collection<String>, Collection<String>) - Static method in class picard.util.LiftoverUtils
method to swap the reference and alt alleles of a bi-allelic, SNP
SYMDIFF - picard.util.IntervalListTools.Action
 
SYNTHETIC_PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
 

T

T - picard.analysis.artifacts.Transition.Base
 
T - picard.illumina.parser.IntensityChannel
 
T - picard.illumina.parser.ReadType
 
TAB_MODE - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
TabbedInputParser - Class in picard.util
Parser for tab-delimited files
TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
Constructor
TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
Constructor
TabbedTextFileWithHeaderParser - Class in picard.util
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
 
TabbedTextFileWithHeaderParser.Row - Class in picard.util
 
TAG - Variable in class picard.sam.FilterSamReads
 
TAG_DUPLICATE_SET_MEMBERS - Variable in class picard.sam.markduplicates.MarkDuplicates
 
TAG_GROUP_SEPERATOR - Variable in class picard.sam.SamToFastqWithTags
 
TAG_PER_MOLECULAR_INDEX - Variable in class picard.illumina.IlluminaBasecallsToSam
 
TAG_VALUE - Variable in class picard.sam.FilterSamReads
 
TAGGING_POLICY - Variable in class picard.sam.markduplicates.MarkDuplicates
 
TAGS_TO_DROP - Variable in class picard.vcf.LiftoverVcf
 
TAGS_TO_REVERSE - Variable in class picard.vcf.LiftoverVcf
 
TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
 
takeSome(Interval, long, long, double) - Method in interface picard.util.IntervalList.IntervalListScatterer
Figure out how much of the input interval to put into current list and how much to leave for the next interval list.
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
 
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
 
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
 
takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
 
TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
TARGET_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
 
TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
 
TARGET_TERRITORY - Variable in class picard.analysis.directed.PanelMetricsBase
The number of unique bases covered by the intervals of all targets that should be covered
TargetedPcrMetrics - Class in picard.analysis.directed
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
 
TargetedPcrMetricsCollector - Class in picard.analysis.directed
Calculates HS metrics for a given SAM or BAM file.
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
 
TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
 
TargetMetrics - Class in picard.analysis.directed
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetrics() - Constructor for class picard.analysis.directed.TargetMetrics
 
TargetMetricsBase - Class in picard.analysis.directed
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsBase() - Constructor for class picard.analysis.directed.TargetMetricsBase
 
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
 
TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
 
TargetMetricsCollector.Coverage - Class in picard.analysis.directed
A simple class that is used to store the coverage information about an interval.
TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
Collect the Target Metrics for one unit of "accumulation" (i.e.
TARGETS - Variable in class picard.util.BaitDesigner
 
Template - Static variable in enum picard.illumina.parser.ReadType
 
templates - Variable in class picard.illumina.parser.ReadStructure
 
Test - Class in picard
 
Test() - Constructor for class picard.Test
 
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
 
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CrosscheckFingerprints
 
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.ExtractFingerprint
 
TEST_INPUT_READABILITY - Variable in class picard.fingerprint.IdentifyContaminant
 
Testing - Class in picard.cmdline.programgroups
For internal test purposes only.
Testing() - Constructor for class picard.cmdline.programgroups.Testing
 
THEORETICAL_SENSITIVITY - Variable in class picard.analysis.TheoreticalSensitivityMetrics
Estimation of sensitivity at a particular allele fraction.
THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
 
THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
 
THEORETICAL_SENSITIVITY_Q - Variable in class picard.analysis.TheoreticalSensitivityMetrics
Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
theoreticalHetSensitivitySampleSize - Variable in class picard.analysis.WgsMetrics
The sample size used for theoretical het sensitivity.
theoreticalSensitivity(Histogram<Integer>, Histogram<Integer>, int, double, double) - Static method in class picard.analysis.TheoreticalSensitivity
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution and depth distribution.
TheoreticalSensitivity - Class in picard.analysis
Created by David Benjamin on 5/13/15.
TheoreticalSensitivity() - Constructor for class picard.analysis.TheoreticalSensitivity
 
TheoreticalSensitivity.RouletteWheel - Class in picard.analysis
 
TheoreticalSensitivityMetrics - Class in picard.analysis
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
TheoreticalSensitivityMetrics() - Constructor for class picard.analysis.TheoreticalSensitivityMetrics
 
THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
thetaIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
 
THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
 
THREAD_COUNT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
ThreadPoolExecutorUtil - Class in picard.util
 
ThreadPoolExecutorUtil() - Constructor for class picard.util.ThreadPoolExecutorUtil
 
ThreadPoolExecutorWithExceptions - Class in picard.util
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
ThreadPoolExecutorWithExceptions(int) - Constructor for class picard.util.ThreadPoolExecutorWithExceptions
Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.
THREE - picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
 
THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
 
THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
 
THREE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
 
THREE_WAYS_DISAGREEMENT_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The tile, which is determined from the file name
tile - Variable in class picard.sam.util.PhysicalLocationInt
 
Tile - Class in picard.illumina.parser
Represents a tile from TileMetricsOut.bin.
Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
 
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The Tile that is described by this metric
TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
The Tile that is described by this metric.
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
 
TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
The expected name of the tile metrics output file.
TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.BasecallsConverter
A comparator used to sort Illumina tiles in their proper order.
TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
 
tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
 
TileIndex - Class in picard.illumina.parser
Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
TileIndex.TileIndexRecord - Class in picard.illumina.parser
 
tileIsSet() - Method in class picard.illumina.parser.ClusterData
 
tileLimit(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
Configures the total number of tiles that the converter will process.
tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
 
TileMetricsOutReader - Class in picard.illumina.parser.readers
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
Return a TileMetricsOutReader for the specified file
TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
Helper class which captures the combination of a lane, tile & metric code
TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
TileMetricsOutReader.TileMetricsVersion - Enum in picard.illumina.parser.readers
 
TileMetricsUtil - Class in picard.illumina.parser
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
 
TilePhasingValue - Class in picard.illumina.parser
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
 
tiles - Variable in class picard.illumina.BasecallsConverter
 
tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
 
TileTemplateRead - Enum in picard.illumina.parser
Defines the first or second template read for a tile
TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
 
TN - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The TN (true negative) count across all variants
TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
toClassName(String) - Method in class picard.cmdline.ClassFinder
Convert a filename to a class name by removing '.class' and converting '/'s to '.'s.
toCode() - Method in enum picard.pedigree.Sex
Returns the code used to encode this sex in a ped/fam file.
TOP - picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
 
TOP_GENOMIC_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
 
toPath() - Method in class picard.nio.PicardHtsPath
Resolve the URI of this object to a Path object.
toPaths(Collection<PicardHtsPath>) - Static method in class picard.nio.PicardHtsPath
Create a List from PicardHtsPaths
toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
toString() - Method in enum picard.analysis.artifacts.Transition
 
toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
 
toString() - Method in class picard.arrays.illumina.ArraysControlInfo
 
toString() - Method in class picard.arrays.illumina.IlluminaManifestRecord
 
toString() - Method in class picard.fingerprint.HaplotypeBlock
 
toString() - Method in class picard.fingerprint.Snp
 
toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
 
toString() - Method in class picard.illumina.parser.ClusterData
 
toString() - Method in class picard.illumina.parser.Range
 
toString() - Method in class picard.illumina.parser.ReadDescriptor
 
toString() - Method in class picard.illumina.parser.ReadStructure
Converts this object into a String using rules complementary to the single string constructor above.
toString() - Method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
 
toString() - Method in class picard.sam.util.Pair
 
toString() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
toString() - Method in class picard.vcf.processor.VcfPathSegment
 
toSymbol() - Method in enum picard.pedigree.Sex
Returns the single-character symbol used to encode sex in a VCF file
TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of basecalls observed at all sites.
TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of bases in all reads
TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of bases assigned to the index.
TOTAL_BASES - Variable in class picard.sam.SamErrorMetric.ErrorMetric
The total number of bases included in the calculation of this metric
TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
The total number of clusters that were seen in the gc bias calculation.
TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of clusters assigned to the index.
TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing complex indel calls that were examined
TOTAL_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
The total number of variants in a particular sample that have a GQ score of 0.
TOTAL_HET_DEPTH - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing indel calls that were examined
TOTAL_MENDELIAN_VIOLATIONS - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
The total of all mendelian violations observed.
TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing multi-allelic SNP calls that were examined
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The total Phred-scaled Q-score for this artifact.
TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The total Phred-scaled Q-score for this artifact.
TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
The total number of reads including all PF and non-PF reads.
TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
The total number of reads in the input file
TOTAL_READS - Variable in class picard.analysis.directed.PanelMetricsBase
The total number of reads in the SAM or BAM file examined.
TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
The total number of reads assigned to the index.
TOTAL_READS_IN_INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
 
TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
The total number of sites that had at least one base covering them.
TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
Number of times this CpG site was encountered
TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
The number of passing bi-allelic SNPs calls (i.e.
totalCycles - Variable in class picard.illumina.parser.ReadStructure
 
totalScore - Variable in class picard.arrays.illumina.InfiniumEGTFile
 
TP - picard.vcf.GenotypeConcordanceStates.ContingencyState
 
TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The TP (true positive) count across all variants
TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
 
trackOpticalDuplicates(List<? extends ReadEnds>, ReadEnds, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.
Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
 
TRANSCRIPT_NAME - picard.annotation.RefFlatReader.RefFlatColumns
 
transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
 
transcriptionStart - Variable in class picard.annotation.Gene.Transcript
 
Transition - Enum in picard.analysis.artifacts
Enum representation of a transition from one base to any other.
Transition.Base - Enum in picard.analysis.artifacts
 
transitionOf(char, char) - Static method in enum picard.analysis.artifacts.Transition
Gets a the enum representing the transition from a 'reference' to a 'call' base.
TRIALLELIC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
TRIMMING_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
 
TRIOS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
triSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
the rate of heterogeneity within tripleton sets
triSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
the rate of homogeneity within tripleton sets.
TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
 
TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
 
TRUSEQ_SMALLRNA - picard.util.IlluminaUtil.IlluminaAdapterPair
 
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
 
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The name of the 'truth' sample
TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The name of the 'truth' sample
TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The state of the 'truth' sample (i.e.
TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
 
truthAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
 
truthAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
 
truthAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
 
TruthAndCallStates(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Constructor for class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
truthState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
 
TT - picard.fingerprint.DiploidGenotype
 
TtoA - picard.analysis.artifacts.Transition
 
TtoC - picard.analysis.artifacts.Transition
 
TtoG - picard.analysis.artifacts.Transition
 
TtoT - picard.analysis.artifacts.Transition
 
TVAL - Variable in class picard.arrays.BafRegressMetrics
The test statistic for the estimate
TWO - picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
 
twoBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
TX_END - picard.annotation.RefFlatReader.RefFlatColumns
 
TX_START - picard.annotation.RefFlatReader.RefFlatColumns
 
type - Variable in class picard.illumina.parser.ReadDescriptor
 
TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
Defines an Illumina template read number (first or second)

U

uByteToInt(byte) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned byte to a signed int
uByteToShort(byte) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned byte to a signed short
uIntToFloat(int) - Static method in class picard.util.UnsignedTypeUtil
 
uIntToLong(int) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned int to a long
UMI_BASE_QUALITIES - Variable in class picard.sam.markduplicates.UmiMetrics
Estimation of Phred scaled quality scores for UMIs
UMI_METRICS_FILE - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
UMI_TAG_NAME - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
UmiAwareMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
UmiAwareMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
 
UmiGraph - Class in picard.sam.markduplicates
UmiGraph is used to identify UMIs that come from the same original source molecule.
UmiMetrics - Class in picard.sam.markduplicates
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
UmiMetrics() - Constructor for class picard.sam.markduplicates.UmiMetrics
 
UmiMetrics(String) - Constructor for class picard.sam.markduplicates.UmiMetrics
 
UmiMetrics(String, double, int, int, int, int, int, double, double, double, double) - Constructor for class picard.sam.markduplicates.UmiMetrics
 
Unaligned - picard.sam.ViewSam.AlignmentStatus
 
UNEXPECTED_MATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
 
UNEXPECTED_MISMATCH - picard.fingerprint.CrosscheckMetric.FingerprintResult
 
unfilteredBaseQHistogram - Variable in class picard.analysis.WgsMetrics
The count of bases observed with a given base quality.
unfilteredBaseQHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
Count of bases observed with a given base quality.
unfilteredDepthHistogram - Variable in class picard.analysis.WgsMetrics
Count of sites with a given depth of coverage.
unfilteredDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
Count of sites with a given depth of coverage.
UNION - picard.util.IntervalListTools.Action
 
UNIQUE - Variable in class picard.util.BedToIntervalList
 
UNIQUE - Variable in class picard.util.IntervalListTools
 
Unknown - picard.pedigree.Sex
 
UNKNOWN - picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
 
UNKNOWN - picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Read whose consensus status cannot be determined.
UNKNOWN - picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
 
UNKNOWN - Static variable in class picard.metrics.MultiLevelCollector
 
UNKNOWN_SEX - Static variable in class picard.pedigree.PedFile
 
UNMAP_CONTAMINANT_READS - Variable in class picard.sam.MergeBamAlignment
 
UNMAPPED_BAM - Variable in class picard.sam.MergeBamAlignment
 
UNMAPPED_BOTH - picard.sam.util.SamComparison.AlignmentComparison
 
UNMAPPED_BOTH - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are not mapped in either file.
UNMAPPED_LEFT - picard.sam.util.SamComparison.AlignmentComparison
 
UNMAPPED_LEFT - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are mapped in right file and found but not mapped in left file
UNMAPPED_READ_STRATEGY - Variable in class picard.sam.MergeBamAlignment
 
UNMAPPED_READS - Variable in class picard.sam.DuplicationMetrics
The total number of unmapped reads examined.
UNMAPPED_RIGHT - picard.sam.util.SamComparison.AlignmentComparison
 
UNMAPPED_RIGHT - Variable in class picard.sam.SamComparisonMetric
The number of primary records which are mapped in left file and found but not mapped in right file
UNPAIRED - picard.analysis.AlignmentSummaryMetrics.Category
 
UNPAIRED_FASTQ - Variable in class picard.sam.SamToFastq
 
UNPAIRED_READ_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
The number of fragments that were marked as duplicates.
UNPAIRED_READS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
Returns the next position info.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.ClocsFileReader
Grab the next set of offset values, decompress them.
unsafeNextInfo() - Method in class picard.illumina.parser.readers.LocsFileReader
 
unsafeNextInfo() - Method in class picard.illumina.parser.readers.PosFileReader
Read a line of text and parse it into two float values, create a PositionInfo and return it
UnsignedTypeUtil - Class in picard.util
A utility class for dealing with unsigned types.
UnsignedTypeUtil() - Constructor for class picard.util.UnsignedTypeUtil
 
UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
UnsortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor, Integer) - Constructor for class picard.illumina.UnsortedBasecallsConverter
Constructs a new BasecallsConverter object.
UNSUPPORTED_GENOME_BUILD - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
 
updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
 
updateMetric(SamComparison.AlignmentComparison) - Method in class picard.sam.SamComparisonMetric
 
updateMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Method in class picard.illumina.BasecallsConverter
 
UpdateVcfSequenceDictionary - Class in picard.vcf
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
UpdateVcfSequenceDictionary() - Constructor for class picard.vcf.UpdateVcfSequenceDictionary
 
URI - Variable in class picard.sam.CreateSequenceDictionary
 
USAGE - Static variable in class picard.illumina.IlluminaBasecallsToSam
 
USAGE - Variable in class picard.sam.ViewSam
 
USAGE_SUMMARY - Static variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
USE_FAST_ALGORITHM - Variable in class picard.analysis.CollectWgsMetrics
 
USE_FIRST - picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
 
USE_JDK_DEFLATER - Variable in class picard.cmdline.CommandLineProgram
 
USE_JDK_INFLATER - Variable in class picard.cmdline.CommandLineProgram
 
USE_OQ - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
USE_OQ - Variable in class picard.analysis.CollectOxoGMetrics
 
USE_ORIGINAL_QUALITIES - Variable in class picard.analysis.CollectQualityYieldMetrics
 
USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
 
USE_SEQUENTIAL_FASTQS - Variable in class picard.sam.FastqToSam
 
USE_THREADING - Variable in class picard.sam.MergeSamFiles
 
USE_VCF_INDEX - Variable in class picard.vcf.GenotypeConcordance
 
useLegacyParser() - Static method in class picard.cmdline.CommandLineProgram
Return true if the legacy Picard command line parser should be used in place of the Barclay command line parser, otherwise, false.
usesNoRefReads() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
 
usesNoRefReads() - Method in class picard.analysis.CollectInsertSizeMetrics
 
usesNoRefReads() - Method in class picard.analysis.CollectQualityYieldMetrics
Ensure that we get all reads regardless of alignment status.
usesNoRefReads() - Method in class picard.analysis.SinglePassSamProgram
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
usesNoRefReads() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
 
uShortToInt(short) - Static method in class picard.util.UnsignedTypeUtil
Convert an unsigned short to an Int
UTR - picard.annotation.LocusFunction
 
UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.

V

VALID_ALLELES - Static variable in class picard.arrays.illumina.IlluminaManifest
 
VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
 
validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
Validates that there are no counts for NA states in the underlying scheme
ValidateSamFile - Class in picard.sam
This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
 
ValidateSamFile.Mode - Enum in picard.sam
 
validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
Check that all cells in the scheme exist.
VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
 
value - Variable in enum picard.arrays.illumina.IlluminaGenotype
 
valueOf(String) - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.artifacts.Transition.Base
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.artifacts.Transition
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.CollectMultipleMetrics.Program
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.analysis.MetricAccumulationLevel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.LocusFunction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.IlluminaGenotype
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.CrosscheckMetric.DataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.DiploidGenotype
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.DiploidHaplotype
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.DistanceMetric
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaDataType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.IntensityChannel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.ReadType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.parser.TileTemplateRead
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.nio.PathProvider
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.pedigree.Sex
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.FilterSamReads.Filter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.RevertSam.FileType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.util.SamComparison.AlignmentComparison
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ValidateSamFile.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.AlignmentStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.sam.ViewSam.PfStatus
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.BaitDesigner.DesignStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalList.IntervalListScatterMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.IntervalListTools.Action
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.util.VariantType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
Returns the enum constant of this type with the specified name.
values() - Static method in enum picard.analysis.AlignmentSummaryMetrics.Category
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.artifacts.Transition.Base
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.artifacts.Transition
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.CollectMultipleMetrics.Program
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.analysis.MetricAccumulationLevel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.LocusFunction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.annotation.RefFlatReader.RefFlatColumns
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.IlluminaGenotype
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.CrosscheckMetric.DataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.CrosscheckMetric.FingerprintResult
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.DiploidGenotype
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.DiploidHaplotype
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.fingerprint.HaplotypeProbabilities.Genotype
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.DistanceMetric
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaDataType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IlluminaMetricsCode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.IntensityChannel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.ReadType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.parser.TileTemplateRead
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.nio.PathProvider
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.pedigree.Sex
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.FilterSamReads.Filter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.CheckDuplicateMarking.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.markduplicates.MarkDuplicates.DuplicateType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.RevertSam.FileType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.util.SamComparison.AlignmentComparison
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ValidateSamFile.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.AlignmentStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.sam.ViewSam.PfStatus
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.BaitDesigner.DesignStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IlluminaUtil.IlluminaAdapterPair
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalList.IntervalListScatterMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.IntervalListTools.Action
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.util.VariantType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStateCodes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.CallState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.ContingencyState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.GenotypeConcordanceStates.TruthState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
Returns an array containing the constants of this enum type, in the order they are declared.
VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
VARIANT_ID_METHOD - Static variable in class picard.vcf.VcfToIntervalList
 
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
The type of the event (i.e.
VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
The type of the event (i.e.
VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,​RESULT> - Interface in picard.vcf.processor
Describes the functionality for an executor that manages the delegation of work to VariantProcessor.Accumulators.
VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,​R> - Class in picard.vcf.processor
A VariantAccumulatorExecutor that breaks down work into chunks described by the provided VariantIteratorProducer and spreads them over the indicated number of threads.
VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
 
VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
 
VariantEvaluationProgramGroup - Class in picard.cmdline.programgroups
Tools that evaluate and refine variant calls, e.g.
VariantEvaluationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantEvaluationProgramGroup
 
VariantFilter - Interface in picard.vcf.filter
Interface for classes that can generate filters for VariantContexts.
VariantFilteringProgramGroup - Class in picard.cmdline.programgroups
Tools that filter variants
VariantFilteringProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantFilteringProgramGroup
 
VariantIteratorProducer - Class in picard.vcf.processor
A mechanism for iterating over CloseableIterator of VariantContexts in in some fashion, given VCF files and optionally an interval list.
VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
 
VariantManipulationProgramGroup - Class in picard.cmdline.programgroups
Tools that manipulate variant call format (VCF) data
VariantManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantManipulationProgramGroup
 
VariantProcessor<RESULT,​ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor
Describes an object that processes variants and produces a result.
VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
Handles VariantContexts, and accumulates their data in some fashion internally.
VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,​RESULT> - Interface in picard.vcf.processor
Generates instances of VariantProcessor.Accumulators.
VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,​R> - Class in picard.vcf.processor
Simple builder of VariantProcessors.
VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
Takes a collection of results produced by VariantProcessor.Accumulator.result() and merges them into a single RESULT.
VariantType - Enum in picard.util
Enum to hold the possible types of dbSnps.
VC_FILTERED - picard.vcf.GenotypeConcordanceStates.CallState
 
VC_FILTERED - picard.vcf.GenotypeConcordanceStates.TruthState
 
VC_FILTERED_CODE - picard.vcf.GenotypeConcordanceStateCodes
 
vcf() - Method in class picard.vcf.processor.VcfFileSegment
Deprecated.
 
vcf() - Method in class picard.vcf.processor.VcfPathSegment
 
VCF - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
 
VCF - Variable in class picard.arrays.VcfToAdpc
 
VCF - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
 
VCF_DIR - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
 
VcfFileSegment - Class in picard.vcf.processor
Deprecated.
from 2022-03-17, Use VcfPathSegment
VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
Deprecated.
 
VcfFileSegmentGenerator - Class in picard.vcf.processor
Deprecated.
from 2022-03-17, Use VcfPathSegmentGenerator
VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
Deprecated.
 
VcfFormatConverter - Class in picard.vcf
Converts an ASCII VCF file to a binary BCF or vice versa.
VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
 
VcfPathSegment - Class in picard.vcf.processor
Describes a segment of a particular VCF file.
VcfPathSegment() - Constructor for class picard.vcf.processor.VcfPathSegment
 
VcfPathSegmentGenerator - Class in picard.vcf.processor
Describes a mechanism for producing VcfPathSegments from a VCF file path.
VcfPathSegmentGenerator() - Constructor for class picard.vcf.processor.VcfPathSegmentGenerator
 
VcfToAdpc - Class in picard.arrays
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
VcfToAdpc() - Constructor for class picard.arrays.VcfToAdpc
 
VcfToIntervalList - Class in picard.vcf
Converts a VCF or BCF file to a Picard Interval List.
VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
 
VcfToIntervalList.VARIANT_ID_TYPES - Enum in picard.vcf
 
VcfUtils - Class in picard.vcf
Created by farjoun on 4/1/17.
VcfUtils() - Constructor for class picard.vcf.VcfUtils
 
VERBOSE - picard.sam.ValidateSamFile.Mode
 
VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
 
verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
expectedCycles are not checked in this implementation.
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
 
verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
 
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
 
verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
 
VerifyIDIntensityContaminationMetrics - Class in picard.arrays
 
VerifyIDIntensityContaminationMetrics() - Constructor for class picard.arrays.VerifyIDIntensityContaminationMetrics
 
version - Variable in class picard.illumina.parser.readers.FilterFileReader
Version number found in the FilterFile, this should equal 3
version - Variable in enum picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
 
ViewSam - Class in picard.sam
Prints a SAM or BAM file to the screen.
ViewSam() - Constructor for class picard.sam.ViewSam
 
ViewSam.AlignmentStatus - Enum in picard.sam
 
ViewSam.PfStatus - Enum in picard.sam
 

W

WARN_ON_MISSING_CONTIG - Variable in class picard.vcf.LiftoverVcf
 
WgsMetrics - Class in picard.analysis
Metrics for evaluating the performance of whole genome sequencing experiments.
WgsMetrics() - Constructor for class picard.analysis.WgsMetrics
Create an instance of this metric that is not mergeable.
WgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.WgsMetrics
Create an instance of this metric that is mergeable.
WgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
 
WgsMetricsProcessor - Interface in picard.analysis
Interface for processing data and generate result for CollectWgsMetrics
WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
Implementation of WgsMetricsProcessor that gets input data from a given iterator and processes it with a help of collector
WgsMetricsProcessorImpl(AbstractLocusIterator<T, AbstractLocusInfo<T>>, ReferenceSequenceFileWalker, AbstractWgsMetricsCollector<T>, ProgressLogger) - Constructor for class picard.analysis.WgsMetricsProcessorImpl
 
WgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
 
WgsMetricsWithNonZeroCoverage(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
 
WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
 
WHOLE_GENOME - picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
 
WIDTH_OF_10_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
WIDTH_OF_20_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
WIDTH_OF_30_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
WIDTH_OF_40_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
WIDTH_OF_50_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
WIDTH_OF_60_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
WIDTH_OF_70_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
WIDTH_OF_80_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
WIDTH_OF_90_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
WIDTH_OF_95_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 95% of all read pairs.
WIDTH_OF_99_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
WINDOW_SIZE - Variable in class picard.analysis.GcBiasSummaryMetrics
The window size on the genome used to calculate the GC of the sequence.
WINDOWS - Variable in class picard.analysis.GcBiasDetailMetrics
The number of windows on the reference genome that have this G+C content.
withApplyEamssFiltering(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
Configures whether or not the converter will apply EAMSS filtering.
withAsyncWriterPool(AsyncWriterPool) - Method in class picard.illumina.BasecallsConverterBuilder
 
withBarcodeExtractor(BarcodeExtractor) - Method in class picard.illumina.BasecallsConverterBuilder
 
withBarcodesDir(File) - Method in class picard.illumina.BasecallsConverterBuilder
Configure the director used to find barcode files created by ExtractIlluminaBarcodes.
withBclQualityEvaluationStrategy(BclQualityEvaluationStrategy) - Method in class picard.illumina.BasecallsConverterBuilder
Configures the bcl quality evaluation strategy that the converter will apply.
withDemultiplex(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
Configures whether or not the converter will demultiplex reads by barcode.
withIgnoreUnexpectedBarcodes(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
Configures whether or not the converter will ignore unexpected barcodes or throw an exception if one is found.
withIncludeNonPfReads(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
Configures whether or not the converter will ignore non-PF reads.
withInput(File...) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
withInput(PicardHtsPath...) - Method in class picard.vcf.processor.VariantProcessor.Builder
 
withMaxRecordsInRam(int) - Method in class picard.illumina.BasecallsConverterBuilder
Specify the max number of records in RAM.
withMolecularIndexQualityTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
Sets the SAM tag to use to store the molecular index base qualities.
withMolecularIndexTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
Sets the SAM tag to use to store the molecular index bases.
withoutChromosomes(Set<String>) - Method in class picard.fingerprint.HaplotypeMap
Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
withSorting(Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, List<File>) - Method in class picard.illumina.BasecallsConverterBuilder
Builds a new sorting basecalls converter.
withTagPerMolecularIndex(List<String>) - Method in class picard.illumina.ClusterDataToSamConverter
Sets the SAM tags to use to store the bases each molecular index.
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst context.
WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst context.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst post-context.
WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst post-context.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
The Q-score for the worst pre-context.
WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
The Q-score for the worst pre-context.
write(byte[], int, int) - Method in class picard.util.CircularByteBuffer
Write bytes into the buffer from the supplied array.
write(DataOutputStream) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
 
write(File) - Method in class picard.pedigree.PedFile
Writes a set of pedigrees out to disk.
write(Iterable<IlluminaAdpcFileWriter.Record>) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
 
write(OUTPUT_RECORD) - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
Write out a single record of type OUTPUT_RECORD.
write(IlluminaAdpcFileWriter.Record) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
 
WRITE_ORIGINAL_ALLELES - Variable in class picard.vcf.LiftoverVcf
 
WRITE_ORIGINAL_POSITION - Variable in class picard.vcf.LiftoverVcf
 
WRITE_READS_FILES - Variable in class picard.sam.FilterSamReads
 
writeAlignment(SAMRecord) - Method in class picard.sam.FixMateInformation
 
writeAsVcf(File, File) - Method in class picard.fingerprint.HaplotypeMap
 
writeBfqFiles() - Method in class picard.fastq.SamToBfqWriter
Writes the binary fastq file(s) to the output directory
writeFingerPrint(Fingerprint, File, File, String, String) - Static method in class picard.fingerprint.FingerprintUtils
A function that takes a Fingerprint and writes it as a VCF to a file
writeReport(File) - Method in class picard.sam.util.SamComparison
 
writeReport(File, List<Header>) - Method in class picard.sam.util.SamComparison
 
writerPool - Variable in class picard.illumina.BasecallsConverter
 
writeToFile(File) - Method in class picard.fingerprint.HaplotypeMap
Writes out a HaplotypeMap file with the contents of this map.

X

x - Variable in class picard.sam.util.PhysicalLocationInt
 
X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
X - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The X coordinate of the read within the tile
xIsSet() - Method in class picard.illumina.parser.ClusterData
 
xPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The x-position as it occurs in the file being read
xQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)

Y

y - Variable in class picard.sam.util.PhysicalLocationInt
 
Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
Y - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
The Y coordinate of the read within the tile
yIsSet() - Method in class picard.illumina.parser.ClusterData
 
yPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The y-position as it occurs in the file being read
yQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)

Z

ZCALL_THRESHOLDS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ZCALL_THRESHOLDS_FILE - Variable in class picard.arrays.MergePedIntoVcf
 
ZCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
The version of ZCall used for calling this sample
ZCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ZCALL_VERSION - Variable in class picard.arrays.MergePedIntoVcf
 
ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.PanelMetricsBase
The fraction of targets that did not reach coverage=1 over any base.
ZEROED_OUT_ASSAY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ZTHRESH_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
ZTHRESH_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
 
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