picard.analysis

Class CollectWgsMetrics.WgsMetricsCollector

java.lang.Object

picard.analysis.CollectWgsMetrics.WgsMetricsCollector

Direct Known Subclasses:

CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

Enclosing class:

CollectWgsMetrics

protected class CollectWgsMetrics.WgsMetricsCollector
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
protected int	coverageCap
protected long[]	histogramArray

Constructor Summary

Constructors

Constructor and Description
WgsMetricsCollector(int coverageCap)

Method Summary

Modifier and Type	Method and Description
protected void	addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file)
void	addInfo(htsjdk.samtools.util.SamLocusIterator.LocusInfo info, htsjdk.samtools.reference.ReferenceSequence ref)
protected void	addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
void	addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)
protected htsjdk.samtools.util.Histogram<java.lang.Integer>	getDepthHistogram()
protected CollectWgsMetrics.WgsMetrics	getMetrics(htsjdk.samtools.util.Histogram<java.lang.Integer> depthHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

histogramArray

protected final long[] histogramArray

coverageCap

protected final int coverageCap

Constructor Detail

WgsMetricsCollector

public WgsMetricsCollector(int coverageCap)

Method Detail

addInfo

public void addInfo(htsjdk.samtools.util.SamLocusIterator.LocusInfo info,
                    htsjdk.samtools.reference.ReferenceSequence ref)

addToMetricsFile

public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file,
                             boolean includeBQHistogram,
                             CountingFilter dupeFilter,
                             CountingFilter mapqFilter,
                             CountingPairedFilter pairFilter)

addBaseQHistogram

protected void addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file)

addMetricsToFile

protected void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,java.lang.Integer> file,
                                CountingFilter dupeFilter,
                                CountingFilter mapqFilter,
                                CountingPairedFilter pairFilter)

getDepthHistogram

protected htsjdk.samtools.util.Histogram<java.lang.Integer> getDepthHistogram()

getMetrics

protected CollectWgsMetrics.WgsMetrics getMetrics(htsjdk.samtools.util.Histogram<java.lang.Integer> depthHistogram,
                                                  CountingFilter dupeFilter,
                                                  CountingFilter mapqFilter,
                                                  CountingPairedFilter pairFilter)