public class CollectQualityYieldMetrics extends SinglePassSamProgram
Modifier and Type | Class and Description |
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static class |
CollectQualityYieldMetrics.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM file
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Modifier and Type | Field and Description |
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boolean |
INCLUDE_SECONDARY_ALIGNMENTS |
boolean |
INCLUDE_SUPPLEMENTAL_ALIGNMENTS |
boolean |
USE_ORIGINAL_QUALITIES |
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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CollectQualityYieldMetrics() |
Modifier and Type | Method and Description |
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protected void |
acceptRead(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref)
Should be implemented by subclasses to accept SAMRecords one at a time.
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protected void |
finish()
Should be implemented by subclasses to do one-time finalization work.
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protected void |
setup(htsjdk.samtools.SAMFileHeader header,
java.io.File samFile)
Should be implemented by subclasses to do one-time initialization work.
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protected boolean |
usesNoRefReads()
Ensure that we get all reads regardless of alignment status.
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doWork, makeItSo
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="OQ", doc="If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field.") public boolean USE_ORIGINAL_QUALITIES
@Option(doc="If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file.") public boolean INCLUDE_SECONDARY_ALIGNMENTS
protected boolean usesNoRefReads()
usesNoRefReads
in class SinglePassSamProgram
protected void setup(htsjdk.samtools.SAMFileHeader header, java.io.File samFile)
SinglePassSamProgram
setup
in class SinglePassSamProgram
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
SinglePassSamProgram
acceptRead
in class SinglePassSamProgram
protected void finish()
SinglePassSamProgram
finish
in class SinglePassSamProgram