CloseableIterator<SAMRecord>
, Closeable
, AutoCloseable
, Iterator<SAMRecord>
public class MergingSamRecordIterator extends Object implements CloseableIterator<SAMRecord>
Constructor | Description |
---|---|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
boolean forcePresorted) |
Deprecated.
|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
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,
Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted) |
Add a set of SAM file iterators to the merging iterator.
|
Modifier and Type | Method | 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.
|
stream, toList
forEachRemaining
@Deprecated public MergingSamRecordIterator(SamFileHeaderMerger headerMerger, boolean forcePresorted)
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, 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, 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 AutoCloseable
close
in interface Closeable
close
in interface CloseableIterator<SAMRecord>
public boolean hasNext()
public SAMRecord next()
public void remove()
public SAMFileHeader getMergedHeader()