Package picard.analysis.replicates
Class IndependentReplicateMetric
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.analysis.replicates.IndependentReplicateMetric
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public class IndependentReplicateMetric extends MergeableMetricBase
A class to store information relevant for biological rate estimation
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
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Constructor Summary
Constructors Constructor Description IndependentReplicateMetric()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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Field Detail
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nSites
public Integer nSites
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nThreeAllelesSites
public Integer nThreeAllelesSites
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nTotalReads
public Integer nTotalReads
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nDuplicateSets
public Integer nDuplicateSets
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nExactlyTriple
public Integer nExactlyTriple
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nExactlyDouble
public Integer nExactlyDouble
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nReadsInBigSets
public Integer nReadsInBigSets
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nDifferentAllelesBiDups
public Integer nDifferentAllelesBiDups
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nReferenceAllelesBiDups
public Integer nReferenceAllelesBiDups
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nAlternateAllelesBiDups
public Integer nAlternateAllelesBiDups
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nDifferentAllelesTriDups
public Integer nDifferentAllelesTriDups
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nMismatchingAllelesBiDups
public Integer nMismatchingAllelesBiDups
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nReferenceAllelesTriDups
public Integer nReferenceAllelesTriDups
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nAlternateAllelesTriDups
public Integer nAlternateAllelesTriDups
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nMismatchingAllelesTriDups
public Integer nMismatchingAllelesTriDups
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nReferenceReads
public Integer nReferenceReads
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nAlternateReads
public Integer nAlternateReads
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nMismatchingUMIsInDiffBiDups
public Integer nMismatchingUMIsInDiffBiDups
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nMatchingUMIsInDiffBiDups
public Integer nMatchingUMIsInDiffBiDups
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nMismatchingUMIsInSameBiDups
public Integer nMismatchingUMIsInSameBiDups
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nMatchingUMIsInSameBiDups
public Integer nMatchingUMIsInSameBiDups
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nMismatchingUMIsInCoOrientedBiDups
public Integer nMismatchingUMIsInCoOrientedBiDups
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nMismatchingUMIsInContraOrientedBiDups
public Integer nMismatchingUMIsInContraOrientedBiDups
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nBadBarcodes
public Integer nBadBarcodes
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nGoodBarcodes
public Integer nGoodBarcodes
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biSiteHeterogeneityRate
public Double biSiteHeterogeneityRate
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triSiteHeterogeneityRate
public Double triSiteHeterogeneityRate
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biSiteHomogeneityRate
public Double biSiteHomogeneityRate
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triSiteHomogeneityRate
public Double triSiteHomogeneityRate
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independentReplicationRateFromBiDups
public Double independentReplicationRateFromBiDups
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independentReplicationRateFromTriDups
public Double independentReplicationRateFromTriDups
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pSameUmiInIndependentBiDup
public Double pSameUmiInIndependentBiDup
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pSameAlleleWhenMismatchingUmi
public Double pSameAlleleWhenMismatchingUmi
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independentReplicationRateFromUmi
public Double independentReplicationRateFromUmi
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replicationRateFromReplicateSets
public Double replicationRateFromReplicateSets
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Method Detail
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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 withNoMergingKeepsValue
.- Overrides:
calculateDerivedFields
in classMergeableMetricBase
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