content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2021 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
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   * 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:
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   * The above copyright notice and this permission notice shall be included in
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  package juicebox.tools.utils.original.stats;
  
  import juicebox.data.ChromosomeHandler;
  import juicebox.tools.utils.original.Chunk;
  import juicebox.tools.utils.original.FragmentCalculation;
  import juicebox.tools.utils.original.mnditerator.AlignmentPairLong;
  import juicebox.tools.utils.original.mnditerator.AsciiPairIterator;
  
  import java.io.IOException;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  public class ParallelStatisticsWorker extends StatisticsWorker {
  
      private final ChromosomeHandler localHandler;
  
      public ParallelStatisticsWorker(String siteFile, List<String> statsFiles, List<Integer> mapqThresholds,
                                      String ligationJunction, String inFile, ChromosomeHandler localHandler,
                                      FragmentCalculation chromosomes) {
          super(siteFile, statsFiles, mapqThresholds, ligationJunction, inFile, chromosomes);
          this.localHandler = localHandler;
      }
  
      public void infileStatistics(Chunk chunk) {
          //read in infile and calculate statistics
          try {
              //create index for AsciiIterator
              Map<String, Integer> chromosomeIndexes = new HashMap<>();
              for (int i = 0; i < localHandler.size(); i++) {
                  chromosomeIndexes.put(localHandler.getChromosomeFromIndex(i).getName(), i);
              }
              //iterate through input file
              AsciiPairIterator files = new AsciiPairIterator(inFile, chromosomeIndexes, chunk, localHandler);
              if (files.hasNext()) {
                  AlignmentPairLong firstPair = (AlignmentPairLong) files.next();
                  String previousBlock = firstPair.getChr1() + "_" + firstPair.getChr2();
                  processSingleEntry(firstPair, previousBlock, true);
                  while (files.hasNext()) {
                      AlignmentPairLong pair = (AlignmentPairLong) files.next();
                      if (processSingleEntry(pair, previousBlock, true)) {
                          break;
                      }
                  }
              }
  
          } catch (IOException e) {
              e.printStackTrace();
          }
      }
  
      protected String getChromosomeNameFromIndex(int chr) {
          return localHandler.getChromosomeFromIndex(chr).getName();
      }
  }
  