Uses of Class
picard.sam.markduplicates.util.LibraryIdGenerator

Packages that use LibraryIdGenerator

Package	Description
picard.sam.markduplicates
picard.sam.markduplicates.util

Uses of LibraryIdGenerator in picard.sam.markduplicates

Fields in picard.sam.markduplicates declared as LibraryIdGenerator

Modifier and Type	Field and Description
protected LibraryIdGenerator	MarkDuplicates.libraryIdGenerator

Methods in picard.sam.markduplicates that return LibraryIdGenerator

Modifier and Type	Method and Description
LibraryIdGenerator	MarkDuplicatesWithMateCigarIterator.getLibraryIdGenerator()

Uses of LibraryIdGenerator in picard.sam.markduplicates.util

Methods in picard.sam.markduplicates.util with parameters of type LibraryIdGenerator

Modifier and Type	Method and Description
protected void	AbstractMarkDuplicatesCommandLineProgram.finalizeAndWriteMetrics(LibraryIdGenerator libraryIdGenerator) Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
ReadEndsForMateCigar	MarkQueue.poll(htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer, htsjdk.samtools.SAMFileHeader header, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator) The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
static void	AbstractMarkDuplicatesCommandLineProgram.trackOpticalDuplicates(java.util.List<? extends ReadEnds> ends, ReadEnds keeper, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator) Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.