Package picard.sam.SamErrorMetric
Interface BaseCalculator
- All Known Implementing Classes:
BaseErrorCalculator
,IndelErrorCalculator
,OverlappingReadsErrorCalculator
,SimpleErrorCalculator
public interface BaseCalculator
An interface that can take a collection of bases (provided as
SamLocusIterator.RecordAndOffset
and SamLocusAndReferenceIterator.SAMLocusAndReference
) and generates a
ErrorMetric
from them.
The Calculator has a suffix which will be used to generate the metric file suffixes.
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Method Summary
Modifier and TypeMethodDescriptionvoid
addBase
(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo) 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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Method Details
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getSuffix
String getSuffix()The suffix that pertains to the implementation of aggregation -
getMetric
ErrorMetric getMetric()Returns the metric generated by the observed loci -
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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