htsjdk.samtools

Class MergingSamRecordIterator

java.lang.Object

htsjdk.samtools.MergingSamRecordIterator

All Implemented Interfaces:

CloseableIterator<SAMRecord>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<SAMRecord>

public class MergingSamRecordIterator
extends java.lang.Object
implements CloseableIterator<SAMRecord>

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

Constructors

Constructor and Description
MergingSamRecordIterator(SamFileHeaderMerger headerMerger, boolean forcePresorted) Deprecated. replaced by MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)
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.

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

MergingSamRecordIterator

@Deprecated
public MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
                                            boolean forcePresorted)

Deprecated. replaced by MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)

Constructs a new merging iterator with the same set of readers and sort order as provided by the header merger parameter.

Parameters:

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.

MergingSamRecordIterator

public 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.

Parameters:

headerMerger - The merged header and contents of readers.

assumeSorted - false ensures that the iterator checks the headers of the readers for appropriate sort order.

MergingSamRecordIterator

public MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
                                java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
                                boolean assumeSorted)

Add a set of SAM file iterators to the merging iterator. Use this to restrict the merged iteration to a given genomic interval, rather than iterating over every read in the backing file or stream.

Parameters:

headerMerger - The merged header and contents of readers.

iterators - Iterator traversing over reader contents.

Method Detail

close

public void close()

Close down all open iterators.

Specified by:

close in interface CloseableIterator<SAMRecord>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Returns true if any of the underlying iterators has more records, otherwise false.

Specified by:

hasNext in interface java.util.Iterator<SAMRecord>

next

public SAMRecord next()

Returns the next record from the top most iterator during merging.

Specified by:

next in interface java.util.Iterator<SAMRecord>

remove

public void remove()

Unsupported operation.

Specified by:

remove in interface java.util.Iterator<SAMRecord>

getMergedHeader

public SAMFileHeader getMergedHeader()

Returns the merged header that the merging iterator is working from.