Package org.broadinstitute.hellbender.utils.read.markduplicates

Class GATKDuplicationMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.MergeableMetricBase

picard.sam.DuplicationMetrics

org.broadinstitute.hellbender.utils.read.markduplicates.GATKDuplicationMetrics

All Implemented Interfaces:

Serializable

public final class GATKDuplicationMetrics
extends DuplicationMetrics
implements Serializable

Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

Field Summary

Fields inherited from class picard.sam.DuplicationMetrics

ESTIMATED_LIBRARY_SIZE, LIBRARY, PERCENT_DUPLICATION, READ_PAIR_DUPLICATES, READ_PAIR_OPTICAL_DUPLICATES, READ_PAIRS_EXAMINED, SECONDARY_OR_SUPPLEMENTARY_RDS, UNMAPPED_READS, UNPAIRED_READ_DUPLICATES, UNPAIRED_READS_EXAMINED

Constructor Summary

Constructors

Constructor	Description
GATKDuplicationMetrics()

Method Summary

Modifier and Type	Method	Description
GATKDuplicationMetrics	copy()
void	updateMetrics(htsjdk.samtools.SAMRecord rec)	Update metrics given a record or GATKRead
void	updateMetrics(GATKRead read)

Methods inherited from class picard.sam.DuplicationMetrics

addDuplicateReadToMetrics, addReadToLibraryMetrics, calculateDerivedFields, calculateDerivedMetrics, calculateRoiHistogram, estimateLibrarySize, estimateRoi, main

Methods inherited from class picard.analysis.MergeableMetricBase

canMerge, merge, merge, mergeIfCan

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

GATKDuplicationMetrics

public GATKDuplicationMetrics()

Method Details

copy

public GATKDuplicationMetrics copy()

updateMetrics

public void updateMetrics(htsjdk.samtools.SAMRecord rec)

Update metrics given a record or GATKRead

updateMetrics

public void updateMetrics(GATKRead read)