public class CollectGcBiasMetrics extends SinglePassSamProgram
Modifier and Type | Field and Description |
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java.io.File |
CHART_OUTPUT |
boolean |
IS_BISULFITE_SEQUENCED |
java.util.Set<MetricAccumulationLevel> |
METRIC_ACCUMULATION_LEVEL |
double |
MINIMUM_GENOME_FRACTION |
int |
SCAN_WINDOW_SIZE |
java.io.File |
SUMMARY_OUTPUT |
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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CollectGcBiasMetrics() |
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.
|
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="The PDF file to render the chart to.") public java.io.File CHART_OUTPUT
@Option(shortName="S", doc="The text file to write summary metrics to.") public java.io.File SUMMARY_OUTPUT
@Option(shortName="WINDOW_SIZE", doc="The size of the scanning windows on the reference genome that are used to bin reads.") public int SCAN_WINDOW_SIZE
@Option(shortName="MGF", doc="For summary metrics, exclude GC windows that include less than this fraction of the genome.") public double MINIMUM_GENOME_FRACTION
@Option(shortName="BS", doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.") public boolean IS_BISULFITE_SEQUENCED
@Option(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL
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