/*
* 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.SAMRecord;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import java.util.Iterator;
/**
* Verifies that the incoming stream of reads is correctly sorted
*/
public class VerifyingSamIterator implements GATKSAMIterator {
GATKSAMIterator it;
SAMRecord last = null;
boolean checkOrderP = true;
public VerifyingSamIterator(GATKSAMIterator it) {
this.it = it;
}
public boolean hasNext() { return this.it.hasNext(); }
public SAMRecord next() {
SAMRecord cur = it.next();
if ( last != null )
verifyRecord(last, cur);
if ( ! cur.getReadUnmappedFlag() )
last = cur;
return cur;
}
private void verifyRecord( final SAMRecord last, final SAMRecord cur ) {
if ( checkOrderP && isOutOfOrder(last, cur) ) {
this.last = null;
throw new UserException.MissortedBAM(String.format("reads are out of order:%nlast:%n%s%ncurrent:%n%s%n", last.format(), cur.format()) );
}
}
private boolean isOutOfOrder( final SAMRecord last, final SAMRecord cur ) {
if ( last == null || cur.getReadUnmappedFlag() )
return false;
else {
if(last.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX || last.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
throw new UserException.MalformedBAM(last,String.format("read %s has inconsistent mapping information.",last.format()));
if(cur.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX || cur.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START)
throw new UserException.MalformedBAM(last,String.format("read %s has inconsistent mapping information.",cur.format()));
return (last.getReferenceIndex() > cur.getReferenceIndex()) ||
(last.getReferenceIndex().equals(cur.getReferenceIndex()) &&
last.getAlignmentStart() > cur.getAlignmentStart());
}
}
public void remove() {
throw new UnsupportedOperationException("Can not remove records from a SAM file via an iterator!");
}
public void close() {
it.close();
}
public Iterator<SAMRecord> iterator() {
return this;
}
}