@DocumentedFeature public class CollectQualityYieldMetrics extends SinglePassSamProgram
| Modifier and Type | Class | Description |
|---|---|---|
static class |
CollectQualityYieldMetrics.QualityYieldMetrics |
A set of metrics used to describe the general quality of a BAM file
|
static class |
CollectQualityYieldMetrics.QualityYieldMetricsCollector |
| Modifier and Type | Field | Description |
|---|---|---|
boolean |
INCLUDE_SECONDARY_ALIGNMENTS |
|
boolean |
INCLUDE_SUPPLEMENTAL_ALIGNMENTS |
|
boolean |
USE_ORIGINAL_QUALITIES |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITYASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER| Constructor | Description |
|---|---|
CollectQualityYieldMetrics() |
| Modifier and Type | Method | Description |
|---|---|---|
protected void |
acceptRead(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref) |
Should be implemented by subclasses to accept SAMRecords one at a time.
|
protected void |
finish() |
Should be implemented by subclasses to do one-time finalization work.
|
protected void |
setup(htsjdk.samtools.SAMFileHeader header,
File samFile) |
Should be implemented by subclasses to do one-time initialization work.
|
protected boolean |
usesNoRefReads() |
Ensure that we get all reads regardless of alignment status.
|
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParserclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitdoWork, makeItSo, setReferenceSequence@Argument(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
@Argument(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
@Argument(doc="If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file.") public boolean INCLUDE_SUPPLEMENTAL_ALIGNMENTS
protected boolean usesNoRefReads()
usesNoRefReads in class SinglePassSamProgramprotected void setup(htsjdk.samtools.SAMFileHeader header,
File samFile)
SinglePassSamProgramsetup in class SinglePassSamProgramprotected void acceptRead(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref)
SinglePassSamProgramacceptRead in class SinglePassSamProgramprotected void finish()
SinglePassSamProgramfinish in class SinglePassSamProgram