/*
* The MIT License (MIT)
*
* Copyright (c) 2016 University of California San Diego
* Author: Jim Robinson
*
* 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.cram.old;
import com.google.common.io.LittleEndianDataInputStream;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.broad.igv.util.stream.IGVSeekableStreamFactory;
import java.io.IOException;
/**
* Created by jrobinson on 12/9/15.
*/
public class CRAMFileReader {
public static CRAMFile openFile(String path) throws IOException {
SeekableStream stream = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
LittleEndianDataInputStream lis = new LittleEndianDataInputStream(stream);
byte[] mn = new byte[4];
for (int i = 0; i < 4; i++) {
mn[i] = lis.readByte();
}
String magicNumber = new String(mn);
int majorFormatNumber = lis.readUnsignedByte();
int minorFormatNumber = lis.readUnsignedByte();
byte[] fileId = new byte[20];
for (int i = 0; i < 20; i++) {
fileId[i] = lis.readByte();
}
String fileName = new String(fileId);
return new CRAMFile(path, majorFormatNumber, minorFormatNumber, fileName);
}
public static void main(String[] args) throws IOException {
CRAMFile cramFile = openFile(args[0]);
cramFile.readContainerHeader(26);
}
}