Package picard.sam.SamErrorMetric
Class SimpleErrorCalculator
java.lang.Object
picard.sam.SamErrorMetric.BaseErrorCalculator
picard.sam.SamErrorMetric.SimpleErrorCalculator
- All Implemented Interfaces:
BaseCalculator
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addBase
(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) The function by which new loci are "shown" to the calculatorReturns the metric generated by the observed lociThe suffix that pertains to the implementation of aggregation
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Field Details
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nMismatchingBases
protected long nMismatchingBases
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Constructor Details
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SimpleErrorCalculator
public SimpleErrorCalculator()
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Method Details
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addBase
public void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) The function by which new loci are "shown" to the calculator- Specified by:
addBase
in interfaceBaseCalculator
- Overrides:
addBase
in classBaseErrorCalculator
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getSuffix
The suffix that pertains to the implementation of aggregation -
getMetric
Returns the metric generated by the observed loci
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