Package picard.sam.SamErrorMetric
Class ReadBaseStratification.LongShortHomopolymerStratifier
java.lang.Object
picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
- 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
Modifier and TypeMethodDescriptionstratify
(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
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Method Details
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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
- Specified by:
getSuffix
in interfaceReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>
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