content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   *
   * 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 juicebox.tools.clt.old;
  
  import juicebox.HiCGlobals;
  import juicebox.tools.clt.CommandLineParser;
  import juicebox.tools.clt.JuiceboxCLT;
  
  import java.io.*;
  import java.util.regex.Pattern;
  
  
  public class FragmentToBed extends JuiceboxCLT {
  
      private String filename;
  
      public FragmentToBed() {
          super("fragmentToBed <fragmentFile>");
      }
  
      /**
       * Convert a fragment site file to a "bed" file
       *
       * @param filename fragment site file
       * @throws java.io.IOException
       */
      private static void fragToBed(String filename) throws IOException {
          BufferedReader reader = null;
          PrintWriter writer = null;
          try {
              File inputFile = new File(filename);
              reader = new BufferedReader(new FileReader(inputFile), HiCGlobals.bufferSize);
  
              writer = new PrintWriter(new BufferedWriter(new FileWriter(filename + ".bed")));
  
              Pattern pattern = Pattern.compile("\\s");
              String nextLine;
              while ((nextLine = reader.readLine()) != null) {
                  //String[] tokens = pattern.split(nextLine);
                  String[] tokens = splitToList(nextLine);
  
                  String chr = tokens[0];
                  int fragNumber = 0;
                  int beg = Integer.parseInt(tokens[1]) - 1;  // 1 vs 0 based coords
                  for (int i = 2; i < tokens.length; i++) {
                      int end = Integer.parseInt(tokens[i]) - 1;
                      writer.println(chr + "\t" + beg + "\t" + end + "\t" + fragNumber);
                      beg = end;
                      fragNumber++;
                  }
  
              }
          } finally {
              if (reader != null) reader.close();
          }
  
      }
  
      @Override
      public void readArguments(String[] args, CommandLineParser parser) {
          //setUsage("juicebox fragmentToBed <fragmentFile>");
          if (args.length != 2) {
              printUsageAndExit();
          }
          filename = args[1];
      }
  
      @Override
      public void run() {
          try {
              fragToBed(filename);
          } catch (Exception e) {
              e.printStackTrace();
          }
      }
  }
  