/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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.broad.igv.sam.reader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.sam.PicardAlignment;
/**
*
*/
class SAMQueryIterator implements CloseableIterator<PicardAlignment> {
String chr;
int start;
int end;
boolean contained;
/**
* SAMRecord is 1-based, PicardAlignment is 0-based
*/
SAMRecord currentRecord;
CloseableIterator<SAMRecord> wrappedIterator;
public SAMQueryIterator(CloseableIterator<SAMRecord> wrappedIterator) {
this.chr = null;
this.wrappedIterator = wrappedIterator;
currentRecord = wrappedIterator.next();
}
/**
*
* @param sequence
* @param start 0-based, inclusive-start
* @param end 0-based, exclusive-end
* @param contained
* @param wrappedIterator
*/
public SAMQueryIterator(String sequence, int start, int end, boolean contained,
CloseableIterator<SAMRecord> wrappedIterator) {
this.chr = sequence;
this.start = start;
this.end = end;
this.contained = contained;
this.wrappedIterator = wrappedIterator;
advanceToFirstRecord();
}
private void advanceToFirstRecord() {
while (wrappedIterator.hasNext()) {
currentRecord = wrappedIterator.next();
if (!currentRecord.getReferenceName().equals(chr)) {
break;
//currentRecord is 1-based, end-inclusive.
//start/end are 0-based, end-exclusive
} else if ((contained && currentRecord.getAlignmentStart()-1 >= start) ||
(!contained && currentRecord.getAlignmentEnd()-1 >= start)) {
break;
}
}
}
public void close() {
wrappedIterator.close();
}
public boolean hasNext() {
if (chr == null && currentRecord != null) {
return true;
}
if (currentRecord == null || (chr != null && !chr.equals(currentRecord.getReferenceName()))) {
return false;
} else {
return contained ? currentRecord.getAlignmentEnd() <= end
: currentRecord.getAlignmentStart() <= end;
}
}
public PicardAlignment next() {
SAMRecord ret = currentRecord;
if (wrappedIterator.hasNext()) {
currentRecord = wrappedIterator.next();
} else {
currentRecord = null;
}
return new PicardAlignment(ret);
}
public void remove() {
//throw new UnsupportedOperationException("Not supported yet.");
}
}