public static class SamPairUtil.SetMateInfoIterator extends PeekableIterator<SAMRecord>
Constructor and Description |
---|
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator)
By default, the mate cigar tag is set
|
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator,
boolean setMateCigar) |
SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator,
boolean setMateCigar,
boolean ignoreMissingMates) |
Modifier and Type | Method and 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.
|
close, remove
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
stream, toList
public SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator)
iterator
- the iterator to wrappublic SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator, boolean setMateCigar)
iterator
- the iterator to wrapsetMateCigar
- 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.public SetMateInfoIterator(java.util.Iterator<SAMRecord> iterator, boolean setMateCigar, boolean ignoreMissingMates)
iterator
- the iterator to wrapsetMateCigar
- 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 encounteredpublic long getNumMateCigarsAdded()
public boolean hasNext()
PeekableIterator
hasNext
in interface java.util.Iterator<SAMRecord>
hasNext
in class PeekableIterator<SAMRecord>
public SAMRecord next()
PeekableIterator
next
in interface java.util.Iterator<SAMRecord>
next
in class PeekableIterator<SAMRecord>
public SAMRecord peek()
PeekableIterator
peek
in class PeekableIterator<SAMRecord>