/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* 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,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* 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,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.gatk.engine.iterators;
import htsjdk.samtools.MergingSamRecordIterator;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMRecord;
import java.util.Iterator;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* 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,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* 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,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* @author aaron
* @version 1.0
* @date Apr 14, 2009
* <p/>
* Class BoundedReadIterator
* <p/>
* This class implements a read iterator that is bounded by the number of reads
* it will produce over the iteration.
*/
public class BoundedReadIterator implements GATKSAMIterator {
// the genome loc we're bounding
final private long readCount;
private long currentCount = 0;
// the iterator we want to decorate
private final GATKSAMIterator iterator;
// our unmapped read flag
private boolean doNotUseThatUnmappedReadPile = false;
/**
* The next read that we've buffered. Null indicates that there's
* nothing in the buffer (not that there isn't a next read).
*/
private SAMRecord record = null;
/**
* constructor
* @param iter
* @param readCount
*/
public BoundedReadIterator(GATKSAMIterator iter, long readCount) {
this.iterator = iter;
this.readCount = readCount;
}
public void useUnmappedReads(boolean useThem) {
this.doNotUseThatUnmappedReadPile = useThem;
}
public SAMFileHeader getHeader() {
// todo: this is bad, we need an iterface out there for samrecords that supports getting the header,
// regardless of the merging
if (iterator instanceof MergingSamRecordIterator)
return ((MergingSamRecordIterator)iterator).getMergedHeader();
else
return null;
}
/**
* Do we have a next? If the iterator has a read and we're not over the read
* count, then yes
* @return
*/
public boolean hasNext() {
if( record != null )
return true;
if (iterator.hasNext() && currentCount < readCount) {
record = iterator.next();
++currentCount;
if (record.getAlignmentStart() == 0 && doNotUseThatUnmappedReadPile) {
return false;
}
return true;
} else {
return false;
}
}
/**
* get the next SAMRecord
* @return SAMRecord representing the next read
*/
public SAMRecord next() {
SAMRecord cached = record;
record = null;
return cached;
}
/**
* this is unsupported on SAMRecord iterators
*/
public void remove() {
throw new UnsupportedOperationException("You cannot use an iterator to remove a SAMRecord");
}
/**
* close the iterator
*/
public void close() {
iterator.close();
}
public Iterator<SAMRecord> iterator() {
return this;
}
}