Package picard.sam.markduplicates

Interface MarkDuplicatesHelper

All Known Implementing Classes:

MarkDuplicates, MarkDuplicatesForFlowHelper, SimpleMarkDuplicatesWithMateCigar, UmiAwareMarkDuplicatesWithMateCigar

public interface MarkDuplicatesHelper

Method Summary

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)

Method Details

generateDuplicateIndexes

void generateDuplicateIndexes(boolean useBarcodes,
 boolean indexOpticalDuplicates)

buildReadEnds

ReadEndsForMarkDuplicates buildReadEnds(htsjdk.samtools.SAMFileHeader header,
 long index,
 htsjdk.samtools.SAMRecord rec,
 boolean useBarcodes)

getReadDuplicateScore

short getReadDuplicateScore(htsjdk.samtools.SAMRecord rec,
 ReadEndsForMarkDuplicates pairedEnds)