Package picard.sam.SamErrorMetric
Class ErrorMetric
- 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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- Direct Known Subclasses:
BaseErrorMetric
,OverlappingErrorMetric
public class ErrorMetric extends MergeableMetricBase
Created by farjoun on 6/26/18.
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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 String
COVARIATE
The value of the covariate define the bases included in this metricprotected static double
PRIOR_ERROR
long
TOTAL_BASES
The total number of bases included in the calculation of this metric
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Constructor Summary
Constructors Constructor Description ErrorMetric()
ErrorMetric(String covariate, long totalBases)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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)
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Methods inherited from class picard.analysis.MergeableMetricBase
calculateDerivedFields, canMerge, merge, merge, mergeIfCan
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Field Detail
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PRIOR_ERROR
protected static double PRIOR_ERROR
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COVARIATE
public String COVARIATE
The value of the covariate define the bases included in this metric
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TOTAL_BASES
public long TOTAL_BASES
The total number of bases included in the calculation of this metric
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Constructor Detail
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ErrorMetric
public ErrorMetric(String covariate, long totalBases)
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ErrorMetric
public ErrorMetric()
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Method Detail
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setPriorError
public static void setPriorError(double priorError)
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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.
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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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