Package picard.sam.SamErrorMetric
Interface BaseCalculator
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- All Known Implementing Classes:
BaseErrorCalculator,IndelErrorCalculator,OverlappingReadsErrorCalculator,SimpleErrorCalculator
public interface BaseCalculatorAn interface that can take a collection of bases (provided asSamLocusIterator.RecordAndOffsetandSamLocusAndReferenceIterator.SAMLocusAndReference) and generates aErrorMetricfrom them.The Calculator has a suffix which will be used to generate the metric file suffixes.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description voidaddBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)The function by which new loci are "shown" to the calculatorErrorMetricgetMetric()Returns the metric generated by the observed lociStringgetSuffix()The suffix that pertains to the implementation of aggregation
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Method Detail
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getSuffix
String getSuffix()
The suffix that pertains to the implementation of aggregation
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getMetric
ErrorMetric getMetric()
Returns the metric generated by the observed loci
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addBase
void addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)The function by which new loci are "shown" to the calculator
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