Package picard.sam.SamErrorMetric
Class ReadBaseStratification.IndelsInReadStratifier
java.lang.Object
picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- All Implemented Interfaces:
ReadBaseStratification.RecordAndOffsetStratifier<Integer>
- Enclosing class:
- ReadBaseStratification
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstratify
(htsjdk.samtools.SAMRecord samRecord) Returns the number of bases associated with I and D CIGAR elements.stratify
(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
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Constructor Details
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IndelsInReadStratifier
public IndelsInReadStratifier()
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Method Details
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stratify
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
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stratify
public Integer 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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