Package picard.sam.SamErrorMetric
Class BaseErrorMetric
- 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.BaseErrorMetric
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- Direct Known Subclasses:
IndelErrorMetric
public class BaseErrorMetric extends ErrorMetric
An error metric for the errors in bases.
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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 long
ERROR_BASES
The number of bases that disagree with the referenceint
Q_SCORE
The (phred) rate of bases that disagree with the reference-
Fields inherited from class picard.sam.SamErrorMetric.ErrorMetric
COVARIATE, PRIOR_ERROR, TOTAL_BASES
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Constructor Summary
Constructors Constructor Description BaseErrorMetric()
BaseErrorMetric(String covariate, long totalBases, long errorBases)
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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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Constructor Detail
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BaseErrorMetric
public BaseErrorMetric(String covariate, long totalBases, long errorBases)
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BaseErrorMetric
public BaseErrorMetric()
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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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