/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * 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 WARRANTIES 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 javax.swing.*;
import java.io.File;

/**
 * Created by IntelliJ IDEA.
 * User: jrobinso
 * Date: Dec 6, 2009
 * Time: 7:42:01 PM
 * To change this template use File | Settings | File Templates.
 */
public class SamIndexer extends AlignmentIndexer {

    final static int FLAG_COL = 1;
    final static int READ_UNMAPPED_FLAG = 0x4;

    public SamIndexer(File samFile, JProgressBar progressBar, SamIndexCreatorDialog.IndexWorker worker) {
        super(samFile, progressBar, worker);
    }

    int getAlignmentStart(String[] fields) throws NumberFormatException {
        // Get alignmetn start and verify file is sorted.
        int alignmentStart = Integer.parseInt(fields[3].trim()) - 1;
        return alignmentStart;
    }

    int getAlignmentLength(String[] fields) throws NumberFormatException {
        String cigarString = fields[5];
        return SamUtils.getPaddedReferenceLength(cigarString);
    }

    String getChromosome(String[] fields) {
        return fields[2];
    }

    @Override
    boolean isMapped(String[] fields) {
        int flags = Integer.parseInt(fields[FLAG_COL]);
        return (flags & READ_UNMAPPED_FLAG) == 0;
    }
}
