Package picard.sam.SamErrorMetric
Class ReadBaseStratification.IndelsInReadStratifier
- java.lang.Object
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- picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
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- All Implemented Interfaces:
ReadBaseStratification.RecordAndOffsetStratifier<Integer>
- Enclosing class:
- ReadBaseStratification
public static class ReadBaseStratification.IndelsInReadStratifier extends Object
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
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Constructor Summary
Constructors Constructor Description IndelsInReadStratifier()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getSuffix()
Integer
stratify(htsjdk.samtools.SAMRecord samRecord)
Returns the number of bases associated with I and D CIGAR elements.T
stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
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Method Detail
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stratify
public Integer stratify(htsjdk.samtools.SAMRecord samRecord)
Returns the number of bases associated with I and D CIGAR elements.- Parameters:
samRecord
- The read to investigate- Returns:
- The number of bases associated with I and D CIGAR elements, or null if the evaluation of either operation caused an error
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getSuffix
public String getSuffix()
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stratify
public T stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
- Specified by:
stratify
in interfaceReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>>
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