/*
* Copyright (c) 2012 The Broad Institute
*
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* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
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*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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package org.broadinstitute.gatk.utils.sam;
import htsjdk.samtools.MergingSamRecordIterator;
import htsjdk.samtools.SamFileHeaderMerger;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import org.broadinstitute.gatk.engine.iterators.GATKSAMIterator;
import org.broadinstitute.gatk.engine.iterators.GATKSAMIteratorAdapter;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.util.*;
/**
* Simple wrapper class that multiplexes multiple ArtificialSingleSampleReadStreams into a single stream of reads
*
* @author David Roazen
*/
public class ArtificialMultiSampleReadStream implements Iterable<SAMRecord> {
private Collection<ArtificialSingleSampleReadStream> perSampleArtificialReadStreams;
private MergingSamRecordIterator mergingIterator;
public ArtificialMultiSampleReadStream( Collection<ArtificialSingleSampleReadStream> perSampleArtificialReadStreams ) {
if ( perSampleArtificialReadStreams == null || perSampleArtificialReadStreams.isEmpty() ) {
throw new ReviewedGATKException("Can't create an ArtificialMultiSampleReadStream out of 0 ArtificialSingleSampleReadStreams");
}
this.perSampleArtificialReadStreams = perSampleArtificialReadStreams;
}
public Iterator<SAMRecord> iterator() {
// lazy initialization to prevent reads from being created until they're needed
initialize();
return mergingIterator;
}
public GATKSAMIterator getGATKSAMIterator() {
// lazy initialization to prevent reads from being created until they're needed
initialize();
return GATKSAMIteratorAdapter.adapt(mergingIterator);
}
private void initialize() {
Collection<SAMFileReader> perSampleSAMReaders = new ArrayList<SAMFileReader>(perSampleArtificialReadStreams.size());
Collection<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(perSampleArtificialReadStreams.size());
for ( ArtificialSingleSampleReadStream readStream : perSampleArtificialReadStreams ) {
Collection<SAMRecord> thisStreamReads = readStream.makeReads();
SAMFileReader reader = new ArtificialSAMFileReader(readStream.getHeader(),
thisStreamReads.toArray(new SAMRecord[thisStreamReads.size()]));
perSampleSAMReaders.add(reader);
headers.add(reader.getFileHeader());
}
SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, headers, true);
mergingIterator = new MergingSamRecordIterator(headerMerger, perSampleSAMReaders, true);
}
}