/*
* 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.tools.sort;
import org.apache.log4j.Logger;
import org.broad.igv.gwas.GWASParser;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
/**
* @author Jim Robinson
* @date 4/12/12
*/
public class GWASSorter extends AsciiSorter {
static Logger log = Logger.getLogger(GWASSorter.class);
List<String> headerLines = new ArrayList<String>();
private GWASParser.GWASColumns columns;
public GWASSorter(File inputFile, File outputFile) {
super(inputFile, outputFile);
this.columns = new GWASParser.GWASColumns();
findColumns(inputFile);
}
private void findColumns(File inputFile) {
BufferedReader br = null;
try {
br = new BufferedReader(new FileReader(inputFile));
String nextLine;
while ((nextLine = br.readLine()) != null) {
headerLines.add(nextLine);
if (!nextLine.startsWith("#")) {
this.columns.parseHeader(nextLine);
break;
}
}
if (this.columns.chrCol < 0) {
throw new RuntimeException("Could not find chromosome column");
}
if (this.columns.locationCol < 0) {
throw new RuntimeException("Could not find start column");
}
} catch (IOException e) {
log.error("Error reading GWAS file", e);
throw new RuntimeException("Error reading GWAS file" + e.getMessage(), e);
} finally {
if (br != null) try {
br.close();
} catch (IOException e) {
}
}
}
@Override
Parser getParser() {
return new Parser(this.columns.chrCol, this.columns.locationCol, true);
}
@Override
String writeHeader(AsciiLineReader reader, PrintWriter writer) throws IOException {
String nextLine;
while((nextLine = reader.readLine()) != null) {
writer.println(nextLine);
if (!nextLine.startsWith("#")) {
break;
}
}
return null;
}
}