/*
* Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved.
*
* 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.
*
* THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
* WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
* WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
* PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
* OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
* TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
* OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
* ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
* THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
* SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.util.CloseableIterator;
import java.io.File;
import java.io.IOException;
import java.util.Iterator;
/**
* @author jrobinso
*/
public class SAMFileGroup implements Iterable<SAMRecord> {
// Map of chromosome -> file
File[] samFiles;
public SAMFileGroup(File[] samFiles) {
this.samFiles = samFiles;
}
public void close() throws IOException {
throw new UnsupportedOperationException("Not supported yet.");
}
public SAMFileHeader getHeader() {
if (samFiles.length == 0) {
return null;
}
SAMFileReader reader = new SAMFileReader(samFiles[0]);
SAMFileHeader header = reader.getFileHeader();
reader.close();
;
return header;
}
public Iterator<SAMRecord> iterator() {
return new SamGroupIterator();
}
public class SamGroupIterator implements CloseableIterator<SAMRecord> {
int idx;
SAMFileReader currentReader;
CloseableIterator<SAMRecord> currentIter;
SAMRecord next;
SamGroupIterator() {
idx = 0;
advance();
}
public void close() {
throw new UnsupportedOperationException("Not supported yet.");
}
public boolean hasNext() {
return next != null;
}
public SAMRecord next() {
SAMRecord ret = next;
advance();
return ret;
}
private void advance() {
if (currentIter == null || !currentIter.hasNext()) {
if (currentIter != null) {
currentIter.close();
currentIter = null;
}
if (currentReader != null) {
currentReader.close();
}
if (idx < samFiles.length) {
currentReader = new SAMFileReader(samFiles[idx]);
currentIter = currentReader.iterator();
idx++;
}
}
next = currentIter == null ? null : currentIter.next();
}
public void remove() {
throw new UnsupportedOperationException("Not supported yet.");
}
}
}