Package picard.sam.SamErrorMetric
Class OverlappingErrorMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
picard.sam.SamErrorMetric.OverlappingErrorMetric
@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 insert
DISAGREES_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/sequencer DISAGREES_WITH_REFERENCE_ONLY_Q
, and an error rate which
cannot be explained nicely THREE_WAYS_DISAGREEMENT_ONLY_Q
.-
Nested Class Summary
Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
-
Field Summary
FieldsModifier and TypeFieldDescriptionint
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)int
The (phred) rate of bases that disagree with the reference, but agree with their matelong
The number of bases for which an overlapping base from the mate read was foundlong
The number of bases that disagree with both the reference and their mate (which agree with each other)long
The number of bases that disagree with the reference, but agree with their matelong
The number of bases that disagree with both the reference and their mate (which also disagree)int
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
-
Constructor Summary
ConstructorsConstructorDescriptionOverlappingErrorMetric
(String covariate, long nTotalBases, long nTotalBasesWithOverlappingReads, long nDisagreeWithRefAndMate, long nDisagreeWithReferenceOnly, long nThreeWaysDisagreement) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Placeholder method that will calculate the derived fields from the other ones.Methods inherited from class picard.sam.SamErrorMetric.ErrorMetric
computeQScore, computeQScore, setPriorError
Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
-
Field Details
-
NUM_BASES_WITH_OVERLAPPING_READS
public long NUM_BASES_WITH_OVERLAPPING_READSThe number of bases for which an overlapping base from the mate read was found -
NUM_DISAGREES_WITH_REFERENCE_ONLY
public long NUM_DISAGREES_WITH_REFERENCE_ONLYThe number of bases that disagree with the reference, but agree with their mate -
DISAGREES_WITH_REFERENCE_ONLY_Q
public int DISAGREES_WITH_REFERENCE_ONLY_QThe (phred) rate of bases that disagree with the reference, but agree with their mate -
NUM_DISAGREES_WITH_REF_AND_MATE
public long NUM_DISAGREES_WITH_REF_AND_MATEThe number of bases that disagree with both the reference and their mate (which agree with each other) -
DISAGREES_WITH_REF_AND_MATE_ONLY_Q
public int DISAGREES_WITH_REF_AND_MATE_ONLY_QThe (phred) rate of bases that disagree with both the reference and their mate (which agree with each other) -
NUM_THREE_WAYS_DISAGREEMENT
public long NUM_THREE_WAYS_DISAGREEMENTThe number of bases that disagree with both the reference and their mate (which also disagree) -
THREE_WAYS_DISAGREEMENT_ONLY_Q
public int THREE_WAYS_DISAGREEMENT_ONLY_QThe (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
-
-
Constructor Details
-
OverlappingErrorMetric
public OverlappingErrorMetric(String covariate, long nTotalBases, long nTotalBasesWithOverlappingReads, long nDisagreeWithRefAndMate, long nDisagreeWithReferenceOnly, long nThreeWaysDisagreement) -
OverlappingErrorMetric
public OverlappingErrorMetric()
-
-
Method Details
-
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
-