Package picard.sam
Class SamToFastqWithTags
java.lang.Object
picard.cmdline.CommandLineProgram
picard.sam.SamToFastq
picard.sam.SamToFastqWithTags
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
FieldsModifier and TypeFieldDescriptionFields 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
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected String[]
Put any custom command-line validation in an override of this method.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
Methods inherited from class picard.sam.SamToFastq
assertPairedMates, doWork
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 Details
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SEQUENCE_TAG_GROUP
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QUALITY_TAG_GROUP
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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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Constructor Details
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SamToFastqWithTags
public SamToFastqWithTags()
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Method Details
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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
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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