/*
 * The MIT License (MIT)
 *
 * Copyright (c) 2007-2015 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 org.broad.igv.variant.util;

import java.io.*;

/**
 * @author jrobinso
 * @date Apr 25, 2011
 */
public class AutismUtils {


    public static void main(String[] args) throws IOException {
        createSampleMap();
    }

    private static void createLoadXML() throws IOException {
        BufferedReader reader = new BufferedReader(new FileReader("/Users/jrobinso/IGV/autism/bam_locations.txt"));

        PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter("/Users/jrobinso/IGV/autism/bam.xml")));

        String nextLine;
        while ((nextLine = reader.readLine()) != null) {

            String bamPath = nextLine.trim();
            String url = bamPath.replace("/seq", "http://iwww.broadinstitute.org/igvdata");
            String name = (new File(bamPath)).getName().replace(".bam", "");

            writer.println("   <Resource name=\"" + name + "\"");
            writer.println("             path=\"" + url + "\"/>");

        }

        reader.close();
        writer.close();
    }

    private static void createSampleMap() throws IOException {
        BufferedReader reader = new BufferedReader(new FileReader("/Users/jrobinso/IGV/autism/bam_locations.txt"));

        PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter("/Users/jrobinso/IGV/autism/samplemap.txt")));

        String nextLine;
        while ((nextLine = reader.readLine()) != null) {

            String bamPath = nextLine.trim();
            String url = bamPath.replace("/seq", "http://iwww.broadinstitute.org/igvdata");
            String name = (new File(bamPath)).getName().replace(".bam", "");

            writer.println(name + "\t" + url);

        }

        reader.close();
        writer.close();
    }
}