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 ReadEndsForMarkDuplicatesbuildReadEnds(htsjdk.samtools.SAMFileHeader header, long index, htsjdk.samtools.SAMRecord rec, boolean useBarcodes)voidgenerateDuplicateIndexes(boolean useBarcodes, boolean indexOpticalDuplicates)shortgetReadDuplicateScore(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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