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java.lang.Object htsjdk.samtools.MergingSamRecordIterator
public class MergingSamRecordIterator
Provides an iterator interface for merging multiple underlying iterators into a single iterable stream. The underlying iterators/files must all have the same sort order unless the requested output format is unsorted, in which case any combination is valid.
Constructor Summary | |
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MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
boolean forcePresorted)
Deprecated. replaced by (SamFileHeaderMerger, Collection |
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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. |
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MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted)
Add a set of SAM file iterators to the merging iterator. |
Method Summary | |
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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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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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, 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.Method Detail |
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public void close()
close
in interface CloseableIterator<SAMRecord>
close
in interface java.io.Closeable
public 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()
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