Package picard.sam.markduplicates
Class MarkDuplicatesWithMateCigarIterator
java.lang.Object
picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- All Implemented Interfaces:
htsjdk.samtools.SAMRecordIterator
,htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord>
,Closeable
,AutoCloseable
,Iterator<htsjdk.samtools.SAMRecord>
public class MarkDuplicatesWithMateCigarIterator
extends Object
implements htsjdk.samtools.SAMRecordIterator
This will iterate through a coordinate sorted SAM file (iterator) and either mark or
remove duplicates as appropriate. This class relies on the coordinate sort order as
well as the mate cigar (MC) optional SAM tag.
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Constructor Summary
ConstructorsConstructorDescriptionMarkDuplicatesWithMateCigarIterator
(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, List<File> tmpDirs) Initializes the mark duplicates iterator. -
Method Summary
Modifier and TypeMethodDescriptionhtsjdk.samtools.SAMRecordIterator
assertSorted
(htsjdk.samtools.SAMFileHeader.SortOrder sortOrder) Establishes that records returned by this iterator are expected to be in the specified sort order.void
close()
int
long
Useful for statistics after the iterator has been exhausted and closed.htsjdk.samtools.util.Histogram<Short>
boolean
hasNext()
void
logMemoryStats
(htsjdk.samtools.util.Log log) htsjdk.samtools.SAMRecord
next()
void
remove()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface htsjdk.samtools.util.CloseableIterator
stream, toList
Methods inherited from interface java.util.Iterator
forEachRemaining
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Constructor Details
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MarkDuplicatesWithMateCigarIterator
public 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, List<File> tmpDirs) throws PicardException Initializes the mark duplicates iterator.- Parameters:
header
- the SAM headeriterator
- an iterator over the SAM records to consideropticalDuplicateFinder
- the algorithm for optical duplicate detectionduplicateScoringStrategy
- the scoring strategy for choosing duplicates. This cannot be SUM_OF_BASE_QUALITIES.toMarkQueueMinimumDistance
- minimum distance for which to bufferremoveDuplicates
- true to remove duplicates, false to mark duplicatesskipPairsWithNoMateCigar
- true to not return mapped pairs with no mate cigar, false otherwiseblockSize
- the size of the blocks in the underlying buffer/queuetmpDirs
- the temporary directories to use if we spill records to disk- Throws:
PicardException
- if the inputs are not in coordinate sort order
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Method Details
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logMemoryStats
public void logMemoryStats(htsjdk.samtools.util.Log log) -
assertSorted
public htsjdk.samtools.SAMRecordIterator assertSorted(htsjdk.samtools.SAMFileHeader.SortOrder sortOrder) Establishes that records returned by this iterator are expected to be in the specified sort order. If this method has been called, then implementers must throw an IllegalStateException from tmpReadEnds() when a samRecordWithOrdinal is read that violates the sort order. This method may be called multiple times over the course of an iteration, changing the expected sort, if desired -- from the time it is called, it validates whatever sort is set, or stops validating if it is set to null or SAMFileHeader.SortOrder.unsorted. If this method is not called, then no validation of the iterated records is done.- Specified by:
assertSorted
in interfacehtsjdk.samtools.SAMRecordIterator
- Parameters:
sortOrder
- The order in which records are expected to be returned- Returns:
- This SAMRecordIterator
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hasNext
public boolean hasNext() -
next
- Specified by:
next
in interfaceIterator<htsjdk.samtools.SAMRecord>
- Throws:
PicardException
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remove
public void remove() -
close
public void close()- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
- Specified by:
close
in interfacehtsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord>
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getNumRecordsWithNoMateCigar
public long getNumRecordsWithNoMateCigar()Useful for statistics after the iterator has been exhausted and closed. -
getNumDuplicates
public int getNumDuplicates() -
getLibraryIdGenerator
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getOpticalDupesByLibraryId
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