Package picard.sam.SamErrorMetric
Class ReadBaseStratification.LongShortHomopolymerStratifier
- java.lang.Object
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- picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
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- All Implemented Interfaces:
ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>
- Enclosing class:
- ReadBaseStratification
public static class ReadBaseStratification.LongShortHomopolymerStratifier extends Object implements ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not). Read direction and only the preceding bases are taken into account.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getSuffix()
ReadBaseStratification.LongShortHomopolymer
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 ReadBaseStratification.LongShortHomopolymer stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
- Specified by:
stratify
in interfaceReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>
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getSuffix
public String getSuffix()
- Specified by:
getSuffix
in interfaceReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>
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