Program: 146548
Project: 146548
Buggy source:
public void processLinesToDivets(){
  Map<Short,ArrayList<String[]>> holder=new HashMap<>();
  for (  String[] array : lines) {
    short num=Short.parseShort(array[1]);
    if (!holder.containsKey(num))     holder.put(num,new ArrayList<String[]>());
    holder.get(num).add(array);
  }
  short comp=1;
  if (!holder.containsKey(comp)) {
    System.err.println("String_Node_Str");
    return;
  }
  short second=2;
  if (!holder.containsKey(second)) {
    System.err.println("String_Node_Str");
    return;
  }
  for (  String[] first : holder.get(comp)) {
    String forient, fchr=first[4], fstart=first[5], fend=String.valueOf(Integer.parseInt(first[5]) + first[11].length()), fmdz=this.getMDZTag(first,first[11]);
    int fedit=Integer.parseInt(this.getNMITag(first));
    double fprob=1.0d - Math.pow(10d,Double.parseDouble(first[6]) / -10d);
    int fflags=Integer.parseInt(first[3]);
    if ((fflags & 0x10) == 0x10)     forient="String_Node_Str";
 else     forient="String_Node_Str";
    for (    String[] sec : holder.get(second)) {
      if (sec[5].startsWith("String_Node_Str"))       System.out.println(StrUtils.StrArray.Join(sec,"String_Node_Str"));
      String sorient, schr=sec[4], sstart=sec[5], send=String.valueOf(Integer.parseInt(sec[5]) + sec[11].length()), smdz=this.getMDZTag(sec,sec[11]);
      int concordant=0, sedit=Integer.parseInt(this.getNMITag(sec));
      double sprob=1.0d - Math.pow(10d,Double.parseDouble(sec[6]) / -10d);
      int sflags=Integer.parseInt(sec[3]);
      if ((sflags & 0x10) == 0x10)       sorient="String_Node_Str";
 else       sorient="String_Node_Str";
      String svcall=this.generateSVCall(fchr,schr,Integer.parseInt(fstart),Integer.parseInt(sstart),Integer.parseInt(fend),Integer.parseInt(send),forient,sorient);
      if (svcall.equals("String_Node_Str"))       continue;
      double avgphred=stats.calcAvgPhred.calcAvgPhred(first[12],sec[12]);
      divet d=new divet(clone,fchr,fstart,fend,forient,schr,sstart,send,sorient,svcall,String.valueOf((fedit + sedit) / 2d),String.valueOf(avgphred),String.valueOf((sprob + fprob) / 2d),String.valueOf(concordant));
      divets.add(d);
    }
  }
}

Fixed version (ground truth):
public void processLinesToDivets(){
  Map<Short,ArrayList<String[]>> holder=new HashMap<>();
  for (  String[] array : lines) {
    short num=Short.parseShort(array[1]);
    if (!holder.containsKey(num))     holder.put(num,new ArrayList<String[]>());
    holder.get(num).add(array);
  }
  short comp=1;
  if (!holder.containsKey(comp)) {
    return;
  }
  short second=2;
  if (!holder.containsKey(second)) {
    return;
  }
  for (  String[] first : holder.get(comp)) {
    String forient, fchr=first[4], fstart=first[5], fend=String.valueOf(Integer.parseInt(first[5]) + first[11].length()), fmdz=this.getMDZTag(first,first[11]);
    int fedit=Integer.parseInt(this.getNMITag(first));
    double fprob=1.0d - Math.pow(10d,Double.parseDouble(first[6]) / -10d);
    int fflags=Integer.parseInt(first[3]);
    if ((fflags & 0x10) == 0x10)     forient="String_Node_Str";
 else     forient="String_Node_Str";
    for (    String[] sec : holder.get(second)) {
      if (sec[5].startsWith("String_Node_Str"))       System.out.println(StrUtils.StrArray.Join(sec,"String_Node_Str"));
      String sorient, schr=sec[4], sstart=sec[5], send=String.valueOf(Integer.parseInt(sec[5]) + sec[11].length()), smdz=this.getMDZTag(sec,sec[11]);
      int concordant=0, sedit=Integer.parseInt(this.getNMITag(sec));
      double sprob=1.0d - Math.pow(10d,Double.parseDouble(sec[6]) / -10d);
      int sflags=Integer.parseInt(sec[3]);
      if ((sflags & 0x10) == 0x10)       sorient="String_Node_Str";
 else       sorient="String_Node_Str";
      String svcall=this.generateSVCall(fchr,schr,Integer.parseInt(fstart),Integer.parseInt(sstart),Integer.parseInt(fend),Integer.parseInt(send),forient,sorient);
      if (svcall.equals("String_Node_Str"))       continue;
      double avgphred=stats.calcAvgPhred.calcAvgPhred(first[12],sec[12]);
      divet d=new divet(clone,fchr,fstart,fend,forient,schr,sstart,send,sorient,svcall,String.valueOf((fedit + sedit) / 2d),String.valueOf(avgphred),String.valueOf((sprob + fprob) / 2d),String.valueOf(concordant));
      divets.add(d);
    }
  }
}