Package picard.sam.SamErrorMetric
Class OverlappingErrorMetric
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.sam.SamErrorMetric.ErrorMetric
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- picard.sam.SamErrorMetric.OverlappingErrorMetric
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@DocumentedFeature(groupName="Metrics", summary="Metrics") public class OverlappingErrorMetric extends ErrorMetric
An error metric for the errors invovling bases in the overlapping region of a read-pair. The resulting metric includes error rate information which can be assigned to the reading of the molecular insertDISAGREES_WITH_REF_AND_MATE_ONLY_Q
, error rate which can be assigned to events that occured to to the molecular insert before it was loaded onto the flowcell/sequencerDISAGREES_WITH_REFERENCE_ONLY_Q
, and an error rate which cannot be explained nicelyTHREE_WAYS_DISAGREEMENT_ONLY_Q
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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
Fields Modifier and Type Field Description int
DISAGREES_WITH_REF_AND_MATE_ONLY_Q
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)int
DISAGREES_WITH_REFERENCE_ONLY_Q
The (phred) rate of bases that disagree with the reference, but agree with their matelong
NUM_BASES_WITH_OVERLAPPING_READS
The number of bases for which an overlapping base from the mate read was foundlong
NUM_DISAGREES_WITH_REF_AND_MATE
The number of bases that disagree with both the reference and their mate (which agree with each other)long
NUM_DISAGREES_WITH_REFERENCE_ONLY
The number of bases that disagree with the reference, but agree with their matelong
NUM_THREE_WAYS_DISAGREEMENT
The number of bases that disagree with both the reference and their mate (which also disagree)int
THREE_WAYS_DISAGREEMENT_ONLY_Q
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)-
Fields inherited from class picard.sam.SamErrorMetric.ErrorMetric
COVARIATE, PRIOR_ERROR, TOTAL_BASES
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Constructor Summary
Constructors Constructor Description OverlappingErrorMetric()
OverlappingErrorMetric(String covariate, long nTotalBases, long nTotalBasesWithOverlappingReads, long nDisagreeWithRefAndMate, long nDisagreeWithReferenceOnly, long nThreeWaysDisagreement)
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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.sam.SamErrorMetric.ErrorMetric
computeQScore, computeQScore, setPriorError
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
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Field Detail
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NUM_BASES_WITH_OVERLAPPING_READS
public long NUM_BASES_WITH_OVERLAPPING_READS
The number of bases for which an overlapping base from the mate read was found
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NUM_DISAGREES_WITH_REFERENCE_ONLY
public long NUM_DISAGREES_WITH_REFERENCE_ONLY
The number of bases that disagree with the reference, but agree with their mate
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DISAGREES_WITH_REFERENCE_ONLY_Q
public int DISAGREES_WITH_REFERENCE_ONLY_Q
The (phred) rate of bases that disagree with the reference, but agree with their mate
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NUM_DISAGREES_WITH_REF_AND_MATE
public long NUM_DISAGREES_WITH_REF_AND_MATE
The number of bases that disagree with both the reference and their mate (which agree with each other)
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DISAGREES_WITH_REF_AND_MATE_ONLY_Q
public int DISAGREES_WITH_REF_AND_MATE_ONLY_Q
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
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NUM_THREE_WAYS_DISAGREEMENT
public long NUM_THREE_WAYS_DISAGREEMENT
The number of bases that disagree with both the reference and their mate (which also disagree)
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THREE_WAYS_DISAGREEMENT_ONLY_Q
public int THREE_WAYS_DISAGREEMENT_ONLY_Q
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
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Constructor Detail
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OverlappingErrorMetric
public OverlappingErrorMetric(String covariate, long nTotalBases, long nTotalBasesWithOverlappingReads, long nDisagreeWithRefAndMate, long nDisagreeWithReferenceOnly, long nThreeWaysDisagreement)
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OverlappingErrorMetric
public OverlappingErrorMetric()
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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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