/*
* The MIT License
*
* Copyright (c) 2009 The 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 htsjdk.samtools;
import htsjdk.samtools.util.CloseableIterator;
import java.io.File;
/**
* Command line utility for manipulating SAM/BAM files.
*/
public class SAMTools
{
private String mCommand = null;
private File mInputFile = null;
public static void main(final String[] args)
throws Exception {
final int status = new SAMTools().run(args);
if (status != 0) {
System.exit(status);
}
}
private SAMTools() {
}
private void usage() {
System.out.println();
System.out.println("SAMTools version 0.1.0");
System.out.println("Tools for manipulating SAM/BAM files");
System.out.println();
System.out.println("Usage: SAMTools <command> <options...>");
System.out.println();
System.out.println("Commands:");
System.out.println(" help");
System.out.println(" view <file>");
System.out.println();
}
private boolean parseArguments(final String[] args) {
if (args.length == 0) {
usage();
return true;
}
final String command = args[0];
final int argpos = 1;
final int argcount = args.length - argpos;
if (command.equals("help")) {
usage();
return true;
} else if (command.equals("view")) {
if (argcount != 1) {
usage();
return false;
}
mInputFile = new File(args[1]);
if (!mInputFile.exists()) {
System.out.println("Input file not found: " + mInputFile);
return false;
}
} else {
System.out.println("Unrecognized command: " + command);
System.out.println();
usage();
return false;
}
mCommand = command;
return true;
}
private int run(final String[] args)
throws Exception {
if (!parseArguments(args)) {
return 1;
}
if (mCommand == null) {
return 0;
}
if (mCommand.equals("view")) {
return runView();
}
return 1;
}
private int runView() {
final SAMFileReader reader = new SAMFileReader(mInputFile);
final CloseableIterator<SAMRecord> iterator = reader.iterator();
while (iterator.hasNext()) {
final SAMRecord record = iterator.next();
System.out.println(record.format());
}
iterator.close();
return 0;
}
}