/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.tools.sort;
import htsjdk.tribble.readers.AsciiLineReader;
import org.broad.igv.Globals;
import java.io.File;
import java.io.IOException;
import java.io.PrintWriter;
import java.util.Comparator;
/**
* @author jrobinso
*/
public class SAMSorter extends AsciiSorter {
public SAMSorter(File inputFile, File outputFile) {
super(inputFile, outputFile);
}
@Override
Parser getParser() {
return new Parser(2, 3);
}
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine = reader.readLine();
while (nextLine != null && nextLine.startsWith("@")) {
writer.println(nextLine);
nextLine = reader.readLine();
}
// First alignment row
return nextLine;
}
public static Comparator<SortableRecord> ReadNameComparator = new Comparator<SortableRecord>() {
public int compare(SortableRecord o1, SortableRecord o2) {
String[] t1 = Globals.tabPattern.split(o1.getText());
String[] t2 = Globals.tabPattern.split(o2.getText());
return t1[0].compareTo(t2[0]);
}
};
}