picard.analysis.replicates

Class IndependentReplicateMetric

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.MergeableMetricBase

picard.analysis.replicates.IndependentReplicateMetric

public class IndependentReplicateMetric
extends MergeableMetricBase

A class to store information relevant for biological rate estimation

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

Modifier and Type	Field and Description
java.lang.Double	biSiteHeterogeneityRate
java.lang.Double	biSiteHomogeneityRate
java.lang.Double	independentReplicationRateFromBiDups
java.lang.Double	independentReplicationRateFromTriDups
java.lang.Double	independentReplicationRateFromUmi
java.lang.Integer	nAlternateAllelesBiDups
java.lang.Integer	nAlternateAllelesTriDups
java.lang.Integer	nAlternateReads
java.lang.Integer	nBadBarcodes
java.lang.Integer	nDifferentAllelesBiDups
java.lang.Integer	nDifferentAllelesTriDups
java.lang.Integer	nDuplicateSets
java.lang.Integer	nExactlyDouble
java.lang.Integer	nExactlyTriple
java.lang.Integer	nGoodBarcodes
java.lang.Integer	nMatchingUMIsInDiffBiDups
java.lang.Integer	nMatchingUMIsInSameBiDups
java.lang.Integer	nMismatchingAllelesBiDups
java.lang.Integer	nMismatchingAllelesTriDups
java.lang.Integer	nMismatchingUMIsInContraOrientedBiDups
java.lang.Integer	nMismatchingUMIsInCoOrientedBiDups
java.lang.Integer	nMismatchingUMIsInDiffBiDups
java.lang.Integer	nMismatchingUMIsInSameBiDups
java.lang.Integer	nReadsInBigSets
java.lang.Integer	nReferenceAllelesBiDups
java.lang.Integer	nReferenceAllelesTriDups
java.lang.Integer	nReferenceReads
java.lang.Integer	nSites
java.lang.Integer	nThreeAllelesSites
java.lang.Integer	nTotalReads
java.lang.Double	pSameAlleleWhenMismatchingUmi
java.lang.Double	pSameUmiInIndependentBiDup
java.lang.Double	replicationRateFromReplicateSets
java.lang.Double	triSiteHeterogeneityRate
java.lang.Double	triSiteHomogeneityRate

Constructor Summary

Constructors

Constructor and Description
IndependentReplicateMetric()

Method Summary

Modifier and Type	Method and Description
void	calculateDerivedFields() Placeholder method that will calculate the derived fields from the other ones.

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

Field Detail

nSites

public java.lang.Integer nSites

nThreeAllelesSites

public java.lang.Integer nThreeAllelesSites

nTotalReads

public java.lang.Integer nTotalReads

nDuplicateSets

public java.lang.Integer nDuplicateSets

nExactlyTriple

public java.lang.Integer nExactlyTriple

nExactlyDouble

public java.lang.Integer nExactlyDouble

nReadsInBigSets

public java.lang.Integer nReadsInBigSets

nDifferentAllelesBiDups

public java.lang.Integer nDifferentAllelesBiDups

nReferenceAllelesBiDups

public java.lang.Integer nReferenceAllelesBiDups

nAlternateAllelesBiDups

public java.lang.Integer nAlternateAllelesBiDups

nDifferentAllelesTriDups

public java.lang.Integer nDifferentAllelesTriDups

nMismatchingAllelesBiDups

public java.lang.Integer nMismatchingAllelesBiDups

nReferenceAllelesTriDups

public java.lang.Integer nReferenceAllelesTriDups

nAlternateAllelesTriDups

public java.lang.Integer nAlternateAllelesTriDups

nMismatchingAllelesTriDups

public java.lang.Integer nMismatchingAllelesTriDups

nReferenceReads

public java.lang.Integer nReferenceReads

nAlternateReads

public java.lang.Integer nAlternateReads

nMismatchingUMIsInDiffBiDups

public java.lang.Integer nMismatchingUMIsInDiffBiDups

nMatchingUMIsInDiffBiDups

public java.lang.Integer nMatchingUMIsInDiffBiDups

nMismatchingUMIsInSameBiDups

public java.lang.Integer nMismatchingUMIsInSameBiDups

nMatchingUMIsInSameBiDups

public java.lang.Integer nMatchingUMIsInSameBiDups

nMismatchingUMIsInCoOrientedBiDups

public java.lang.Integer nMismatchingUMIsInCoOrientedBiDups

nMismatchingUMIsInContraOrientedBiDups

public java.lang.Integer nMismatchingUMIsInContraOrientedBiDups

nBadBarcodes

public java.lang.Integer nBadBarcodes

nGoodBarcodes

public java.lang.Integer nGoodBarcodes

biSiteHeterogeneityRate

public java.lang.Double biSiteHeterogeneityRate

triSiteHeterogeneityRate

public java.lang.Double triSiteHeterogeneityRate

biSiteHomogeneityRate

public java.lang.Double biSiteHomogeneityRate

triSiteHomogeneityRate

public java.lang.Double triSiteHomogeneityRate

independentReplicationRateFromBiDups

public java.lang.Double independentReplicationRateFromBiDups

independentReplicationRateFromTriDups

public java.lang.Double independentReplicationRateFromTriDups

pSameUmiInIndependentBiDup

public java.lang.Double pSameUmiInIndependentBiDup

pSameAlleleWhenMismatchingUmi

public java.lang.Double pSameAlleleWhenMismatchingUmi

independentReplicationRateFromUmi

public java.lang.Double independentReplicationRateFromUmi

replicationRateFromReplicateSets

public java.lang.Double replicationRateFromReplicateSets

Constructor Detail

IndependentReplicateMetric

public IndependentReplicateMetric()

Method Detail

calculateDerivedFields

public void calculateDerivedFields()

Description copied from class: MergeableMetricBase

Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.

Overrides:

calculateDerivedFields in class MergeableMetricBase