| Package | Description |
|---|---|
| picard.sam.markduplicates | |
| picard.sam.markduplicates.util |
| Constructor and Description |
|---|
MarkDuplicatesWithMateCigarIterator(htsjdk.samtools.SAMFileHeader header,
htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord> iterator,
OpticalDuplicateFinder opticalDuplicateFinder,
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy,
int toMarkQueueMinimumDistance,
boolean removeDuplicates,
boolean skipPairsWithNoMateCigar,
int maxRecordsInRam,
int blockSize,
java.util.List<java.io.File> tmpDirs)
Initializes the mark duplicates iterator.
|
| Modifier and Type | Field and Description |
|---|---|
protected OpticalDuplicateFinder |
AbstractOpticalDuplicateFinderCommandLineProgram.opticalDuplicateFinder |
| Modifier and Type | Method and Description |
|---|---|
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.
|
| Constructor and Description |
|---|
ReadEndsForMateCigar(htsjdk.samtools.SAMFileHeader header,
htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal,
OpticalDuplicateFinder opticalDuplicateFinder,
short libraryId)
Builds a read ends object that represents a single read.
|