public class MarkQueue extends Object
Constructor and Description |
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MarkQueue(htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy) |
Modifier and Type | Method and Description |
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void |
add(ReadEndsForMateCigar other,
htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer,
DuplicationMetrics metrics)
Add a record to the mark queue.
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Set<ReadEnds> |
getLocations(ReadEndsForMateCigar current)
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
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int |
getNumDuplicates()
Returns the number of duplicates detected
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int |
getToMarkQueueMinimumDistance()
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
|
boolean |
isEmpty() |
ReadEndsForMateCigar |
peek()
Returns the first element in this queue
|
ReadEndsForMateCigar |
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.
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void |
setToMarkQueueMinimumDistance(int toMarkQueueMinimumDistance)
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
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boolean |
shouldBeInLocations(ReadEndsForMateCigar current)
Returns true if we should track this for optical duplicate detection, false otherwise
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int |
size()
The number of records currently in this queue.
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public MarkQueue(htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy duplicateScoringStrategy)
public int getNumDuplicates()
public int size()
public boolean isEmpty()
public void setToMarkQueueMinimumDistance(int toMarkQueueMinimumDistance)
public int getToMarkQueueMinimumDistance()
public boolean shouldBeInLocations(ReadEndsForMateCigar current)
public Set<ReadEnds> getLocations(ReadEndsForMateCigar current)
public ReadEndsForMateCigar peek()
public ReadEndsForMateCigar poll(htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer, htsjdk.samtools.SAMFileHeader header, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator)
public void add(ReadEndsForMateCigar other, htsjdk.samtools.util.SamRecordTrackingBuffer outputBuffer, DuplicationMetrics metrics)