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>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<htsjdk.samtools.SAMRecord>

public class MarkDuplicatesWithMateCigarIterator
extends java.lang.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.

Constructor Summary

Constructors

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.

Method Summary

Modifier and Type	Method and Description
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.
void	close()
LibraryIdGenerator	getLibraryIdGenerator()
int	getNumDuplicates()
int	getNumRecordsWithNoMateCigar() Useful for statistics after the iterator has been exhausted and closed.
htsjdk.samtools.util.Histogram<java.lang.Short>	getOpticalDupesByLibraryId()
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

Constructor Detail

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,
                                           java.util.List<java.io.File> tmpDirs)
                                    throws PicardException

Initializes the mark duplicates iterator.

Parameters:

header - the SAM header

iterator - an iterator over the SAM records to consider

opticalDuplicateFinder - the algorithm for optical duplicate detection

duplicateScoringStrategy - the scoring strategy for choosing duplicates. This cannot be SUM_OF_BASE_QUALITIES.

toMarkQueueMinimumDistance - minimum distance for which to buffer

removeDuplicates - true to remove duplicates, false to mark duplicates

skipPairsWithNoMateCigar - true to not return mapped pairs with no mate cigar, false otherwise

blockSize - the size of the blocks in the underlying buffer/queue

tmpDirs - the temporary directories to use if we spill records to disk

Throws:

PicardException - if the inputs are not in coordinate sort order

Method Detail

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 interface htsjdk.samtools.SAMRecordIterator

Parameters:

sortOrder - The order in which records are expected to be returned

Returns:

This SAMRecordIterator

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<htsjdk.samtools.SAMRecord>

next

public htsjdk.samtools.SAMRecord next()
                               throws PicardException

Specified by:

next in interface java.util.Iterator<htsjdk.samtools.SAMRecord>

Throws:

PicardException

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<htsjdk.samtools.SAMRecord>

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getNumRecordsWithNoMateCigar

public int getNumRecordsWithNoMateCigar()

Useful for statistics after the iterator has been exhausted and closed.

getNumDuplicates

public int getNumDuplicates()

getLibraryIdGenerator

public LibraryIdGenerator getLibraryIdGenerator()

getOpticalDupesByLibraryId

public htsjdk.samtools.util.Histogram<java.lang.Short> getOpticalDupesByLibraryId()