107 lines
2.9 KiB
Java
107 lines
2.9 KiB
Java
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/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2008 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever.
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* Neither the Broad Institute nor MIT can be responsible for its use, misuse,
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* or functionality.
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*/
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package edu.mit.broad.sam;
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import edu.mit.broad.sam.util.CloseableIterator;
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import java.io.*;
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/**
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* Command line utility for manipulating SAM/BAM files.
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*/
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public class SAMTools
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{
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private String mCommand = null;
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private File mInputFile = null;
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public static void main(final String[] args)
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throws Exception {
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final int status = new SAMTools().run(args);
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if (status != 0) {
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System.exit(status);
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}
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}
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private SAMTools() {
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}
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private void usage() {
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System.out.println();
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System.out.println("SAMTools version 0.1.0");
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System.out.println("Tools for manipulating SAM/BAM files");
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System.out.println();
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System.out.println("Usage: SAMTools <command> <options...>");
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System.out.println();
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System.out.println("Commands:");
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System.out.println(" help");
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System.out.println(" view <file>");
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System.out.println();
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}
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private boolean parseArguments(final String[] args) {
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if (args.length == 0) {
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usage();
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return true;
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}
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final String command = args[0];
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final int argpos = 1;
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final int argcount = args.length - argpos;
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if (command.equals("help")) {
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usage();
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return true;
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} else if (command.equals("view")) {
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if (argcount != 1) {
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usage();
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return false;
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}
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mInputFile = new File(args[1]);
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if (!mInputFile.exists()) {
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System.out.println("Input file not found: " + mInputFile);
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return false;
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}
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} else {
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System.out.println("Unrecognized command: " + command);
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System.out.println();
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usage();
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return false;
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}
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mCommand = command;
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return true;
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}
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private int run(final String[] args)
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throws Exception {
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if (!parseArguments(args)) {
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return 1;
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}
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if (mCommand == null) {
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return 0;
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}
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if (mCommand.equals("view")) {
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return runView();
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}
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return 1;
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}
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private int runView() {
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final SAMFileReader reader = new SAMFileReader(mInputFile);
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final CloseableIterator<SAMRecord> iterator = reader.iterator();
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while (iterator.hasNext()) {
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final SAMRecord record = iterator.next();
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System.out.println(record.format());
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}
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iterator.close();
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return 0;
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}
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}
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