/*
* Copyright (c) 2007-2012 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broad.igv.sam.EmptyAlignmentIterator;
import org.broad.igv.sam.PicardAlignment;
import org.broad.igv.ui.util.MessageUtils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
/**
* @author jrobinso
*/
public class BAMFileReader implements AlignmentReader<PicardAlignment> {
private static Logger log = Logger.getLogger(BAMFileReader.class);
SAMFileReader reader;
SAMFileHeader header;
public BAMFileReader(File bamFile) {
try {
File indexFile = findIndexFile(bamFile);
reader = new SAMFileReader(bamFile, indexFile);
reader.setValidationStringency(ValidationStringency.SILENT);
loadHeader();
} catch (Exception e) {
MessageUtils.showMessage("Error loading SAM header: " + e.getMessage());
e.printStackTrace();
}
}
public SAMFileHeader getFileHeader() {
if (header == null) {
loadHeader();
}
return header;
}
public List<String> getSequenceNames() {
SAMFileHeader header = getFileHeader();
if (header == null) {
return null;
}
List<String> seqNames = new ArrayList();
List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
if (records.size() > 0) {
for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
String chr = rec.getSequenceName();
seqNames.add(chr);
}
}
return seqNames;
}
public Set<String> getPlatforms() {
return AlignmentReaderFactory.getPlatforms(getFileHeader());
}
private void loadHeader() {
header = reader.getFileHeader();
}
public void close() throws IOException {
reader.close();
}
public boolean hasIndex() {
return reader.hasIndex();
}
public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) {
SAMRecordIterator query = null;
try {
query = reader.query(sequence, start + 1, end, contained);
return new WrappedIterator(query);
} catch (ArrayIndexOutOfBoundsException e) {
log.error("Error querying BAM file ", e);
MessageUtils.showMessage("Error reading bam file. This usually indicates a problem with the index (bai) file." +
"<br>" + e.toString() + " (" + e.getMessage() + ")");
return EmptyAlignmentIterator.getInstance();
}
}
public CloseableIterator<PicardAlignment> iterator() {
return new WrappedIterator(reader.iterator());
}
/**
* Look for BAM index file according to standard naming convention. Slightly modified version of Picard
* function of the same name.
*
* @param dataFile BAM file name.
* @return Index file name, or null if not found.
*/
private static File findIndexFile(final File dataFile) {
final String bamPath = dataFile.getAbsolutePath();
// foo.bam.bai
String bai = bamPath + ".bai";
File indexFile1 = new File(bai);
if (indexFile1.length() > 0) {
return indexFile1;
}
// alternate (Picard) convention, foo.bai
final String bamExtension = ".bam";
File indexFile2 = null;
if (bamPath.toLowerCase().endsWith(bamExtension)) {
bai = bamPath.substring(0, bamPath.length() - bamExtension.length()) + ".bai";
indexFile2 = new File(bai);
if (indexFile2.length() > 0) {
return indexFile2;
}
}
log.info("Index file: " + indexFile1.getAbsolutePath() + " not found");
if (indexFile2 != null) log.info("Index file: " + indexFile2.getAbsolutePath() + " not Found");
return null;
}
}