Program: 146549
Project: 146549
Buggy source:
private SetMap<BufferedInitialSet> populateDivets(FlatFile file){
  SetMap<BufferedInitialSet> tSet=new SetMap<>();
  readNameMappings divMaps=new readNameMappings();
  ArrayList<ReadPair> tempholder=new ArrayList<>();
  BufferedReader divetReader=ReaderReturn.openFile(file.getDivet().toFile());
  try {
    String line;
    String[] segs;
    while ((line=divetReader.readLine()) != null) {
      segs=line.split("String_Node_Str");
      if (segs.length < 13)       continue;
      if ((segs[1].equals(this.chr))) {
        divMaps.addRead(segs[0].trim());
        if (!segs[13].equals("String_Node_Str") && Double.valueOf(segs[12]) > pfilter && !segs[9].equals("String_Node_Str") && !segs[9].equals("String_Node_Str")) {
          ReadPair rp=new ReadPair(line,file,readEnum.IsDisc);
          tempholder.add(rp);
        }
      }
    }
  }
 catch (  IOException ex) {
    Logger.getLogger(BufferedReader.class.getName()).log(Level.SEVERE,null,ex);
  }
  int gapCount=0;
  int curSetCount=0;
  for (  ReadPair d : tempholder) {
    d.setMapCount(divMaps.retMap(d.Name()));
    if (this.useGapOverlap) {
      if (gaps.checkGapOverlap(d)) {
        gapCount++;
        continue;
      }
    }
    if (!tSet.checkAndCombinePairs(d)) {
      BufferedInitialSet temp=new BufferedInitialSet(this.buffer,"String_Node_Str");
      temp.bufferedAdd(d);
      tSet.addBedData(temp);
      curSetCount++;
      if (curSetCount % 100000 == 0) {
        log.log(Level.FINE,"String_Node_Str" + curSetCount + "String_Node_Str"+ tempholder.size());
      }
    }
  }
  log.log(Level.INFO,"String_Node_Str" + gapCount + "String_Node_Str");
  return tSet;
}

Fixed version (ground truth):
private SetMap<BufferedInitialSet> populateDivets(FlatFile file){
  SetMap<BufferedInitialSet> tSet=new SetMap<>();
  readNameMappings divMaps=new readNameMappings();
  ArrayList<ReadPair> tempholder=new ArrayList<>();
  BufferedReader divetReader=ReaderReturn.openFile(file.getDivet().toFile());
  try {
    String line;
    String[] segs;
    while ((line=divetReader.readLine()) != null) {
      segs=line.split("String_Node_Str");
      if (segs.length < 13)       continue;
      if ((segs[1].equals(this.chr))) {
        divMaps.addRead(segs[0].trim());
        if (!segs[13].equals("String_Node_Str") && Double.valueOf(segs[12]) > pfilter && !segs[9].equals("String_Node_Str") && !segs[9].equals("String_Node_Str")) {
          ReadPair rp=new ReadPair(line,file,readEnum.IsDisc);
          tempholder.add(rp);
        }
      }
    }
  }
 catch (  IOException ex) {
    Logger.getLogger(BufferedReader.class.getName()).log(Level.SEVERE,null,ex);
  }
  log.log(Level.FINE,"String_Node_Str");
  int gapCount=0;
  int curSetCount=0;
  for (  ReadPair d : tempholder) {
    d.setMapCount(divMaps.retMap(d.Name()));
    if (this.useGapOverlap) {
      if (gaps.checkGapOverlap(d)) {
        gapCount++;
        continue;
      }
    }
    if (!tSet.checkAndCombinePairs(d)) {
      BufferedInitialSet temp=new BufferedInitialSet(this.buffer,"String_Node_Str");
      temp.bufferedAdd(d);
      tSet.addBedData(temp);
      curSetCount++;
      if (curSetCount % 100000 == 0) {
        log.log(Level.FINE,"String_Node_Str" + curSetCount + "String_Node_Str"+ tempholder.size());
      }
    }
  }
  log.log(Level.INFO,"String_Node_Str" + gapCount + "String_Node_Str");
  return tSet;
}