Package picard.sam.SamErrorMetric
Class ErrorMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.MergeableMetricBase
picard.sam.SamErrorMetric.ErrorMetric
- Direct Known Subclasses:
BaseErrorMetric
,OverlappingErrorMetric
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class ErrorMetric
extends MergeableMetricBase
Created by farjoun on 6/26/18.
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Nested Class Summary
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
FieldsModifier and TypeFieldDescriptionThe value of the covariate define the bases included in this metricprotected static double
long
The total number of bases included in the calculation of this metric -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
computeQScore
(long numberOfErrors) compute a qscore given the number of errors and the total number of bases.protected int
computeQScore
(long numberOfErrors, long nTotalBases) compute a qscore given the number of errors and the total number of bases.static void
setPriorError
(double priorError) Methods inherited from class picard.analysis.MergeableMetricBase
calculateDerivedFields, canMerge, merge, merge, mergeIfCan
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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PRIOR_ERROR
protected static double PRIOR_ERROR -
COVARIATE
The value of the covariate define the bases included in this metric -
TOTAL_BASES
public long TOTAL_BASESThe total number of bases included in the calculation of this metric
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Constructor Details
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ErrorMetric
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ErrorMetric
public ErrorMetric()
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Method Details
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setPriorError
public static void setPriorError(double priorError) -
computeQScore
protected int computeQScore(long numberOfErrors) compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the numerator and 1/PRIOR_ERROR in the denominator. -
computeQScore
protected int computeQScore(long numberOfErrors, long nTotalBases) compute a qscore given the number of errors and the total number of bases. Uses a false count of 1 int the denominator and 1 in the numerator.
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