Package picard.illumina.quality
Class CollectHiSeqXPfFailMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.illumina.quality.CollectHiSeqXPfFailMetrics
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@DocumentedFeature public class CollectHiSeqXPfFailMetrics extends CommandLineProgram
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter. (BETA)
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
a metric class for describing FP failing reads from an Illumina HiSeqX lane *static class
CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
Metrics produced by the GetHiSeqXPFFailMetrics program.protected static class
CollectHiSeqXPfFailMetrics.ReadClassifier
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Field Summary
Fields Modifier and Type Field Description File
BASECALLS_DIR
static String
detailedMetricsExtension
Integer
LANE
int
N_CYCLES
int
NUM_PROCESSORS
File
OUTPUT
double
PROB_EXPLICIT_READS
static String
summaryMetricsExtension
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectHiSeqXPfFailMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected String[]
customCommandLineValidation()
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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BASECALLS_DIR
@Argument(doc="The Illumina basecalls directory. ", shortName="B") public File BASECALLS_DIR
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OUTPUT
@Argument(shortName="O", doc="Basename for metrics file. Resulting file will be <OUTPUT>.pffail_summary_metrics", optional=false) public File OUTPUT
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PROB_EXPLICIT_READS
@Argument(shortName="P", doc="The fraction of (non-PF) reads for which to output explicit classification. Output file will be <OUTPUT>.pffail_detailed_metrics (if PROB_EXPLICIT_READS != 0)", optional=true) public double PROB_EXPLICIT_READS
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LANE
@Argument(doc="Lane number.", shortName="L") public Integer LANE
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NUM_PROCESSORS
@Argument(shortName="NP", doc="Run this many PerTileBarcodeExtractors in parallel. If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.", optional=true) public int NUM_PROCESSORS
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N_CYCLES
@Argument(doc="Number of cycles to look at. At time of writing PF status gets determined at cycle 24 so numbers greater than this will yield strange results. In addition, PF status is currently determined at cycle 24, so running this with any other value is neither tested nor recommended.", optional=true) public int N_CYCLES
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detailedMetricsExtension
public static final String detailedMetricsExtension
- See Also:
- Constant Field Values
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summaryMetricsExtension
public static final String summaryMetricsExtension
- See Also:
- Constant Field Values
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Method Detail
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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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