| Package | Description |
|---|---|
| picard.sam.markduplicates.util |
| Modifier and Type | Method and Description |
|---|---|
ReadEndsForMateCigar |
MarkQueue.peek()
Returns the first element in this queue
|
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.
|
| Modifier and Type | Method and Description |
|---|---|
void |
PhysicalLocationForMateCigarSet.add(ReadEndsForMateCigar end)
Adds the end to this set, if not already added based on physical location
|
void |
MarkQueue.add(ReadEndsForMateCigar other,
htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer,
DuplicationMetrics metrics)
Add a record to the mark queue.
|
java.util.Set<ReadEnds> |
MarkQueue.getLocations(ReadEndsForMateCigar current)
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
|
void |
PhysicalLocationForMateCigarSet.remove(ReadEndsForMateCigar end)
Removes the end from this set, if present
|
void |
PhysicalLocationForMateCigarSet.replace(ReadEndsForMateCigar current,
ReadEndsForMateCigar other)
Replaces a given end with the other end.
|
boolean |
MarkQueue.shouldBeInLocations(ReadEndsForMateCigar current)
Returns true if we should track this for optical duplicate detection, false otherwise
|
| Constructor and Description |
|---|
ReadEndsForMateCigar(ReadEndsForMateCigar other,
htsjdk.samtools.util.SamRecordWithOrdinal samRecordWithOrdinal)
Creates a shallow copy from the "other"
|