/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* 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.
*
*
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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package org.broad.igv.util.converters;
import org.broad.igv.util.ParsingUtils;
import java.io.*;
import java.util.List;
/**
* Converts a directory of "density" files (Tarjei et al) to bedgraph
*
* @author Jim Robinson
* @date 9/13/11
*/
public class DensitiesToBedGraph {
public static void main(String[] args) throws IOException {
File inputDir = new File(args[0]);
File outputDir = new File(args[1]);
convertAll(inputDir, outputDir);
}
private static void convertAll(File inputDir, File outputDir) throws IOException {
File[] files = inputDir.listFiles();
for (File f : files) {
if (f.getAbsolutePath().endsWith(".densities.txt.gz")) {
String ofile = f.getName().replace(".densities.txt.gz", ".bedgraph");
convert(f, new File(outputDir, ofile));
}
}
}
public static void convert(File ifile, File ofile) throws IOException {
BufferedReader reader = null;
PrintWriter pw = null;
reader = ParsingUtils.openBufferedReader(ifile.getAbsolutePath());
pw = new PrintWriter(new BufferedWriter(new FileWriter(ofile)));
String nextLine;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = nextLine.split("\t");
float counts = Float.parseFloat(tokens[2]);
if (counts > 0) {
int start = Integer.parseInt(tokens[1]);
pw.println(tokens[0] + "\t" + start + "\t" + (start + 25) + "\t" + counts);
}
}
reader.close();
pw.close();
}
}