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.
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close, removeclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitstream, toListpublic 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()
PeekableIteratorhasNext in interface java.util.Iterator<SAMRecord>hasNext in class PeekableIterator<SAMRecord>public SAMRecord next()
PeekableIteratornext in interface java.util.Iterator<SAMRecord>next in class PeekableIterator<SAMRecord>public SAMRecord peek()
PeekableIteratorpeek in class PeekableIterator<SAMRecord>