public class CollectBaseDistributionByCycle extends SinglePassSamProgram
Modifier and Type | Field and Description |
---|---|
boolean |
ALIGNED_READS_ONLY |
java.io.File |
CHART_OUTPUT |
boolean |
PF_READS_ONLY |
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 |
---|
CollectBaseDistributionByCycle() |
Modifier and Type | Method and 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(java.lang.String[] args) |
protected void |
setup(htsjdk.samtools.SAMFileHeader header,
java.io.File samFile)
Should be implemented by subclasses to do one-time initialization work.
|
doWork, makeItSo, usesNoRefReads
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.") public java.io.File CHART_OUTPUT
@Option(doc="If set to true, calculate the base distribution over aligned reads only.") public boolean ALIGNED_READS_ONLY
public static void main(java.lang.String[] args)
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