Package picard.sam.markduplicates
Interface MarkDuplicatesHelper
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- All Known Implementing Classes:
MarkDuplicates
,MarkDuplicatesForFlowHelper
,SimpleMarkDuplicatesWithMateCigar
,UmiAwareMarkDuplicatesWithMateCigar
public interface MarkDuplicatesHelper
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description ReadEndsForMarkDuplicates
buildReadEnds(htsjdk.samtools.SAMFileHeader header, long index, htsjdk.samtools.SAMRecord rec, boolean useBarcodes)
void
generateDuplicateIndexes(boolean useBarcodes, boolean indexOpticalDuplicates)
short
getReadDuplicateScore(htsjdk.samtools.SAMRecord rec, ReadEndsForMarkDuplicates pairedEnds)
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Method Detail
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generateDuplicateIndexes
void generateDuplicateIndexes(boolean useBarcodes, boolean indexOpticalDuplicates)
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buildReadEnds
ReadEndsForMarkDuplicates buildReadEnds(htsjdk.samtools.SAMFileHeader header, long index, htsjdk.samtools.SAMRecord rec, boolean useBarcodes)
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getReadDuplicateScore
short getReadDuplicateScore(htsjdk.samtools.SAMRecord rec, ReadEndsForMarkDuplicates pairedEnds)
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