Package htsjdk.samtools

Class SamPairUtil.SetMateInfoIterator

java.lang.Object

htsjdk.samtools.util.PeekableIterator<SAMRecord>

htsjdk.samtools.SamPairUtil.SetMateInfoIterator

All Implemented Interfaces:

CloseableIterator<SAMRecord>, Closeable, AutoCloseable, Iterator<SAMRecord>

Enclosing class:

SamPairUtil

public static class SamPairUtil.SetMateInfoIterator
extends PeekableIterator<SAMRecord>

A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).

Constructor Summary

Constructors

Constructor	Description
SetMateInfoIterator(Iterator<SAMRecord> iterator)	By default, the mate cigar tag is set
SetMateInfoIterator(Iterator<SAMRecord> iterator, boolean setMateCigar)
SetMateInfoIterator(Iterator<SAMRecord> iterator, boolean setMateCigar, boolean ignoreMissingMates)

Method Summary

Modifier and Type	Method	Description
long	getNumMateCigarsAdded()
boolean	hasNext()	True if there are more items, in which case both next() and peek() will return a value.
SAMRecord	next()	Returns the next object and advances the iterator.
SAMRecord	peek()	Returns the next object but does not advance the iterator.

Methods inherited from class htsjdk.samtools.util.PeekableIterator

close, 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 Details

SetMateInfoIterator

public SetMateInfoIterator(Iterator<SAMRecord> iterator)

By default, the mate cigar tag is set

Parameters:

iterator - the iterator to wrap

SetMateInfoIterator

public SetMateInfoIterator(Iterator<SAMRecord> iterator,
 boolean setMateCigar)

Parameters:

iterator - the iterator to wrap

setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

SetMateInfoIterator

public SetMateInfoIterator(Iterator<SAMRecord> iterator,
 boolean setMateCigar,
 boolean ignoreMissingMates)

Parameters:

iterator - the iterator to wrap

setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

ignoreMissingMates - set this to true if we are to ignore missing mates, otherwise an exception will be thrown when a missing mate is encountered

Method Details

getNumMateCigarsAdded

public long getNumMateCigarsAdded()

Returns:

the current number of mate cigars added. This could be more than the number of records returned.

hasNext

public boolean hasNext()

Description copied from class: PeekableIterator

True if there are more items, in which case both next() and peek() will return a value.

Specified by:

hasNext in interface Iterator<SAMRecord>

Overrides:

hasNext in class PeekableIterator<SAMRecord>

next

public SAMRecord next()

Description copied from class: PeekableIterator

Returns the next object and advances the iterator.

Specified by:

next in interface Iterator<SAMRecord>

Overrides:

next in class PeekableIterator<SAMRecord>

peek

public SAMRecord peek()

Description copied from class: PeekableIterator

Returns the next object but does not advance the iterator. Subsequent calls to peek() and next() will return the same object.

Overrides:

peek in class PeekableIterator<SAMRecord>