Package picard.sam.SamErrorMetric
Interface BaseCalculator
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- All Known Implementing Classes:
BaseErrorCalculator
,IndelErrorCalculator
,OverlappingReadsErrorCalculator
,SimpleErrorCalculator
public interface BaseCalculator
An interface that can take a collection of bases (provided asSamLocusIterator.RecordAndOffset
andSamLocusAndReferenceIterator.SAMLocusAndReference
) and generates aErrorMetric
from 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 void
addBase(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
The function by which new loci are "shown" to the calculatorErrorMetric
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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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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