/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.tools.converters;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.ReadMate;
import org.broad.igv.sam.reader.AlignmentReader;
import org.broad.igv.sam.reader.AlignmentReaderFactory;
import java.io.*;
/**
* Converts a bam -> a bed file by writing each record as a bed feature.
* <p/>
* If the "properPair" option is true paired alignments marked "proper" are output as a single record, with the
* name field containing the insert size.
*
* @author Jim Robinson
* @date 6/4/12
*/
public class BamToBed {
public static void convert(File inputBam, File outputBed, boolean properPairs) throws IOException {
AlignmentReader reader = null;
CloseableIterator<Alignment> iter = null;
PrintWriter bedWriter = null;
int maxInsertSize = 0;
try {
bedWriter = new PrintWriter(new BufferedWriter(new FileWriter(outputBed)));
reader = AlignmentReaderFactory.getReader(inputBam.getAbsolutePath(), false);
iter = reader.iterator();
while (iter.hasNext()) {
Alignment a = iter.next();
if(passFilter(a, properPairs)) {
int start = a.getAlignmentStart();
final int insertSize = Math.abs(a.getInferredInsertSize());
int end = properPairs ? (start + insertSize) : a.getAlignmentEnd();
String name = a.getReadName();
String strand = properPairs ? "." : (a.isNegativeStrand() ? "-" : "+");
bedWriter.print(a.getChr() + "\t" + start + "\t" + end + "\t" + name + "\t" + strand);
if(properPairs) {
bedWriter.println("\t" + insertSize);
}
else {
bedWriter.println();
}
maxInsertSize = insertSize > maxInsertSize ? insertSize : maxInsertSize;
}
}
} finally {
if(bedWriter != null) bedWriter.close();
if(iter != null) iter.close();
if(reader != null) reader.close();
}
}
private static boolean passFilter(Alignment alignment, boolean properPairs) {
// For paired coverage, see if the alignment is properly paired, and if it is the "leftmost" alignment
// (to prevent double-counting the pair).
if(properPairs) {
ReadMate mate = alignment.getMate();
if(!alignment.isProperPair() || alignment.getMate() == null || alignment.getStart() > mate.getStart()) {
return false;
}
}
return alignment.isMapped() && !alignment.isDuplicate() && !alignment.isVendorFailedRead();
}
}