public class MeanQualityByCycle extends SinglePassSamProgram
Modifier and Type | Field | Description |
---|---|---|
boolean |
ALIGNED_READS_ONLY |
|
File |
CHART_OUTPUT |
|
boolean |
PF_READS_ONLY |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER
Constructor | Description |
---|---|
MeanQualityByCycle() |
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, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
doWork, makeItSo, usesNoRefReads
@Option(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.") public File CHART_OUTPUT
@Option(doc="If set to true, calculate mean quality over aligned reads only.") public boolean ALIGNED_READS_ONLY
public static void main(String[] args)
protected void setup(htsjdk.samtools.SAMFileHeader header, 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