public class MergingSamRecordIterator extends java.lang.Object implements CloseableIterator<SAMRecord>
| Constructor and Description |
|---|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
boolean forcePresorted)
Deprecated.
|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Collection<SamReader> readers,
boolean assumeSorted)
Constructs a new merging iterator with the same set of readers and sort order as
provided by the header merger parameter.
|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted)
Add a set of SAM file iterators to the merging iterator.
|
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Close down all open iterators.
|
SAMFileHeader |
getMergedHeader()
Returns the merged header that the merging iterator is working from.
|
boolean |
hasNext()
Returns true if any of the underlying iterators has more records, otherwise false.
|
SAMRecord |
next()
Returns the next record from the top most iterator during merging.
|
void |
remove()
Unsupported operation.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitstream, toList@Deprecated public MergingSamRecordIterator(SamFileHeaderMerger headerMerger, boolean forcePresorted)
MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)headerMerger - The merged header and contents of readers.forcePresorted - True to ensure that the iterator checks the headers of the readers for appropriate sort order.public MergingSamRecordIterator(SamFileHeaderMerger headerMerger, java.util.Collection<SamReader> readers, boolean assumeSorted)
headerMerger - The merged header and contents of readers.assumeSorted - false ensures that the iterator checks the headers of the readers for appropriate sort order.public MergingSamRecordIterator(SamFileHeaderMerger headerMerger, java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators, boolean assumeSorted)
headerMerger - The merged header and contents of readers.iterators - Iterator traversing over reader contents.public void close()
close in interface CloseableIterator<SAMRecord>close in interface java.io.Closeableclose in interface java.lang.AutoCloseablepublic boolean hasNext()
hasNext in interface java.util.Iterator<SAMRecord>public SAMRecord next()
next in interface java.util.Iterator<SAMRecord>public void remove()
remove in interface java.util.Iterator<SAMRecord>public SAMFileHeader getMergedHeader()