Package picard.sam.SamErrorMetric
Class SimpleErrorCalculator
- java.lang.Object
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- picard.sam.SamErrorMetric.BaseErrorCalculator
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- picard.sam.SamErrorMetric.SimpleErrorCalculator
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- All Implemented Interfaces:
BaseCalculator
public class SimpleErrorCalculator extends BaseErrorCalculator
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 Modifier and Type Field Description protected long
nMismatchingBases
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Constructor Summary
Constructors Constructor Description SimpleErrorCalculator()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef)
The function by which new loci are "shown" to the calculatorBaseErrorMetric
getMetric()
Returns the metric generated by the observed lociString
getSuffix()
The suffix that pertains to the implementation of aggregation
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Method Detail
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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
public String getSuffix()
The suffix that pertains to the implementation of aggregation
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getMetric
public BaseErrorMetric getMetric()
Returns the metric generated by the observed loci
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