picard.analysis

Class CollectWgsMetrics.WgsMetricsCollector

java.lang.Object

picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>

picard.analysis.CollectWgsMetrics.WgsMetricsCollector

Direct Known Subclasses:

CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

Enclosing class:

CollectWgsMetrics

protected static class CollectWgsMetrics.WgsMetricsCollector
extends AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>

Field Summary

Fields inherited from class picard.analysis.AbstractWgsMetricsCollector

counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray

Constructor Summary

Constructors

Constructor and Description
WgsMetricsCollector(CollectWgsMetrics metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)

Method Summary

Modifier and Type	Method and Description
void	addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN) Accumulates the data from AbstractLocusInfo in inner structures

Methods inherited from class picard.analysis.AbstractWgsMetricsCollector

addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter

Methods inherited from class java.lang.Object

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

Constructor Detail

WgsMetricsCollector

public WgsMetricsCollector(CollectWgsMetrics metrics,
                           int coverageCap,
                           htsjdk.samtools.util.IntervalList intervals)

Method Detail

addInfo

public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info,
                    htsjdk.samtools.reference.ReferenceSequence ref,
                    boolean referenceBaseN)

Description copied from class: AbstractWgsMetricsCollector

Accumulates the data from AbstractLocusInfo in inner structures

Specified by:

addInfo in class AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>

Parameters:

info - AbstractLocusInfo with aligned to reference position reads

ref - ReferenceSequence

referenceBaseN - true if current the value of reference base represents a no call