CloseableIterator<SAMRecord>
, Closeable
, AutoCloseable
, Iterator<SAMRecord>
public static class SamPairUtil.SetMateInfoIterator extends PeekableIterator<SAMRecord>
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) |
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.
|
stream, toList
forEachRemaining
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
close, remove
public SetMateInfoIterator(Iterator<SAMRecord> iterator)
iterator
- the iterator to wrappublic SetMateInfoIterator(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(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
public SAMRecord next()
PeekableIterator
public SAMRecord peek()
PeekableIterator
peek
in class PeekableIterator<SAMRecord>