Program: 146556
Project: 146556
Buggy source:
/** 
 * This is a main, workhorse method designed to run through the BAM file and calculate the read group average and stdev values.
 * @param input The string of the path to the BAM file to scan
 * @param samplimit A limit on the number of BAM file entries per readgroupto sample statistics from. Higher limits require more memory.
 */
public void ScanFile(String input,int samplimit){
  SAMFileReader sam=new SAMFileReader(new File(input));
  sam.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
  if (!sam.hasIndex()) {
    System.out.println("String_Node_Str");
    BAMIndexer b=new BAMIndexer(new File(input + "String_Node_Str"),sam.getFileHeader());
    sam.enableFileSource(true);
    sam.iterator().forEachRemaining((s) -> {
      b.processAlignment(s);
    }
);
    b.finish();
    sam.close();
    System.out.println("String_Node_Str");
    sam=new SAMFileReader(new File(input));
  }
  header=sam.getFileHeader();
  if (expectRG) {
    List<SAMReadGroupRecord> temp=header.getReadGroups();
    temp.forEach((e) -> rgList.add(e.getId()));
  }
 else   rgList.add("String_Node_Str");
  SAMRecordIterator itr=sam.iterator();
  while (itr.hasNext()) {
    SAMRecord s=itr.next();
    String rgid;
    if (expectRG)     rgid=s.getReadGroup().getId();
 else     rgid="String_Node_Str";
    int rFlags=s.getFlags();
    if ((rFlags & 0x4) == 0x4 || (rFlags & 0x8) == 0x8 || !((rFlags & 0x1) == 0x1))     continue;
    if (s.getInferredInsertSize() == 0)     continue;
    if (!insertSizes.containsKey(rgid))     insertSizes.put(rgid,new ArrayList<>(samplimit));
    if (insertSizes.get(rgid).size() >= samplimit) {
      if (checkIfSamplingDone(samplimit))       break;
    }
 else {
      insertSizes.get(rgid).add(Math.abs(s.getInferredInsertSize()));
    }
  }
  itr.close();
  sam.close();
}

Fixed version (ground truth):
/** 
 * This is a main, workhorse method designed to run through the BAM file and calculate the read group average and stdev values.
 * @param input The string of the path to the BAM file to scan
 * @param samplimit A limit on the number of BAM file entries per readgroupto sample statistics from. Higher limits require more memory.
 */
public void ScanFile(String input,int samplimit){
  SAMFileReader sam=new SAMFileReader(new File(input));
  sam.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
  if (!sam.hasIndex()) {
    System.out.println("String_Node_Str");
    log.log(Level.INFO,"String_Node_Str" + input);
    BAMIndexer b=new BAMIndexer(new File(input + "String_Node_Str"),sam.getFileHeader());
    sam.enableFileSource(true);
    sam.iterator().forEachRemaining((s) -> {
      b.processAlignment(s);
    }
);
    b.finish();
    sam.close();
    System.out.println("String_Node_Str");
    log.log(Level.FINE,"String_Node_Str");
    sam=new SAMFileReader(new File(input));
  }
  header=sam.getFileHeader();
  if (expectRG) {
    List<SAMReadGroupRecord> temp=header.getReadGroups();
    temp.forEach((e) -> rgList.add(e.getId()));
    log.log(Level.FINE,"String_Node_Str" + StrArray.Join((ArrayList<String>)rgList,"String_Node_Str"));
  }
 else {
    rgList.add("String_Node_Str");
    log.log(Level.FINE,"String_Node_Str");
  }
  SAMRecordIterator itr=sam.iterator();
  while (itr.hasNext()) {
    SAMRecord s=itr.next();
    String rgid;
    if (expectRG)     rgid=s.getReadGroup().getId();
 else     rgid="String_Node_Str";
    int rFlags=s.getFlags();
    if ((rFlags & 0x4) == 0x4 || (rFlags & 0x8) == 0x8 || !((rFlags & 0x1) == 0x1))     continue;
    if (s.getInferredInsertSize() == 0)     continue;
    if (!insertSizes.containsKey(rgid))     insertSizes.put(rgid,new ArrayList<>(samplimit));
    if (insertSizes.get(rgid).size() >= samplimit) {
      if (checkIfSamplingDone(samplimit)) {
        log.log(Level.FINE,"String_Node_Str" + rgid);
        break;
      }
    }
 else {
      insertSizes.get(rgid).add(Math.abs(s.getInferredInsertSize()));
    }
  }
  itr.close();
  sam.close();
  log.log(Level.INFO,"String_Node_Str");
}