@DocumentedFeature public class QualityScoreDistribution extends SinglePassSamProgram
| Modifier and Type | Field | Description |
|---|---|---|
boolean |
ALIGNED_READS_ONLY |
|
File |
CHART_OUTPUT |
|
boolean |
INCLUDE_NO_CALLS |
|
boolean |
PF_READS_ONLY |
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 |
|---|---|
QualityScoreDistribution() |
| 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.
|
static void |
main(String[] args) |
Required main method.
|
protected void |
setup(htsjdk.samtools.SAMFileHeader header,
File samFile) |
Should be implemented by subclasses to do one-time initialization work.
|
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, usesNoRefReads@Argument(shortName="CHART",
doc="A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT
@Argument(doc="If set to true calculate mean quality over aligned reads only.") public boolean ALIGNED_READS_ONLY
@Argument(shortName="PF",
doc="If set to true calculate mean quality over PF reads only.")
public boolean PF_READS_ONLY
@Argument(doc="If set to true, include quality for no-call bases in the distribution.") public boolean INCLUDE_NO_CALLS
public static void main(String[] args)
protected 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