Package picard.sam
Class SamToFastqWithTags
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.SamToFastq
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- picard.sam.SamToFastqWithTags
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public class SamToFastqWithTags extends SamToFastq
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. See MAQ FASTQ specification for details.
Usage example:
java -jar picard.jar SamToFastqWithTags I=input.bam FASTQ=output.fastq SEQUENCE_TAG_GROUP="CR" QUALITY_TAG_GROUP="CY" SEQUENCE_TAG_GROUP="CB,UR" QUALITY_TAG_GROUP="CY,UY"
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Field Summary
Fields Modifier and Type Field Description Boolean
COMPRESS_OUTPUTS_PER_TAG_GROUP
List<String>
QUALITY_TAG_GROUP
List<String>
SEQUENCE_TAG_GROUP
List<String>
TAG_GROUP_SEPERATOR
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Fields inherited from class picard.sam.SamToFastq
CLIPPING_ACTION, CLIPPING_ATTRIBUTE, CLIPPING_MIN_LENGTH, COMPRESS_OUTPUTS_PER_RG, FASTQ, INCLUDE_NON_PF_READS, INCLUDE_NON_PRIMARY_ALIGNMENTS, INPUT, INTERLEAVE, OUTPUT_DIR, OUTPUT_PER_RG, QUALITY, RE_REVERSE, READ1_MAX_BASES_TO_WRITE, READ1_TRIM, READ2_MAX_BASES_TO_WRITE, READ2_TRIM, RG_TAG, SECOND_END_FASTQ, UNPAIRED_FASTQ
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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 SamToFastqWithTags()
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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 Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>>
generateAdditionalWriters(List<htsjdk.samtools.SAMReadGroupRecord> readGroups, htsjdk.samtools.fastq.FastqWriterFactory factory)
protected void
handleAdditionalRecords(htsjdk.samtools.SAMRecord currentRecord, Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>> tagWriters, htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)
protected void
initializeAdditionalWriters()
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Methods inherited from class picard.sam.SamToFastq
assertPairedMates, doWork
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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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SEQUENCE_TAG_GROUP
@Argument(shortName="STG", doc="List of comma separated tag values to extract from Input SAM/BAM to be used as read sequence", minElements=1) public List<String> SEQUENCE_TAG_GROUP
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QUALITY_TAG_GROUP
@Argument(shortName="QTG", doc="List of comma separated tag values to extract from Input SAM/BAM to be used as read qualities", optional=true) public List<String> QUALITY_TAG_GROUP
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TAG_GROUP_SEPERATOR
@Argument(shortName="SEP", doc="List of any sequences (e.g. \'AACCTG`) to put in between each comma separated list of sequence tags in each SEQUENCE_TAG_GROUP (STG)", optional=true) public List<String> TAG_GROUP_SEPERATOR
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COMPRESS_OUTPUTS_PER_TAG_GROUP
@Argument(shortName="GZOPTG", doc="Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the file names.") public Boolean COMPRESS_OUTPUTS_PER_TAG_GROUP
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Method Detail
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initializeAdditionalWriters
protected void initializeAdditionalWriters()
- Overrides:
initializeAdditionalWriters
in classSamToFastq
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handleAdditionalRecords
protected void handleAdditionalRecords(htsjdk.samtools.SAMRecord currentRecord, Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>> tagWriters, htsjdk.samtools.SAMRecord read1, htsjdk.samtools.SAMRecord read2)
- Overrides:
handleAdditionalRecords
in classSamToFastq
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generateAdditionalWriters
protected Map<htsjdk.samtools.SAMReadGroupRecord,List<htsjdk.samtools.fastq.FastqWriter>> generateAdditionalWriters(List<htsjdk.samtools.SAMReadGroupRecord> readGroups, htsjdk.samtools.fastq.FastqWriterFactory factory)
- Overrides:
generateAdditionalWriters
in classSamToFastq
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customCommandLineValidation
protected String[] customCommandLineValidation()
Description copied from class:SamToFastq
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 classSamToFastq
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error messages to be written to the appropriate place.
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