Program: 30629
Project: 30629
Buggy source:
/** 
 * Returns a PriorityRunnable that encapsulates the work involved with writing the provided tileRecord's data for the given barcode to disk.
 * @param tile       The tile from which the record was read
 * @param tileRecord The processing record associated with the tile
 * @param barcode    The barcode whose data within the tileRecord is to be written
 * @return The runnable that upon invocation writes the barcode's data from the tileRecord to disk
 */
private PriorityRunnable newBarcodeWorkInstance(final Tile tile,final TileProcessingRecord tileRecord,final String barcode){
  return new PriorityRunnable(){
    @Override public void run(){
      try {
        final SortingCollection<SAMRecord> records=tileRecord.getBarcodeRecords().get(barcode);
        final SAMFileWriter writer=barcodeSamWriterMap.get(barcode);
        log.debug(String.format("String_Node_Str",tile.getNumber(),barcode));
        final PeekIterator<SAMRecord> it=new PeekIterator<SAMRecord>(records.iterator());
        while (it.hasNext()) {
          final SAMRecord rec=it.next();
          if (it.hasNext()) {
            final SAMRecord lookAhead=it.peek();
            if (!rec.getReadUnmappedFlag() || !lookAhead.getReadUnmappedFlag()) {
              throw new IllegalStateException("String_Node_Str");
            }
            if (samRecordQueryNameComparator.compare(rec,lookAhead) == 0) {
              it.next();
              log.info("String_Node_Str" + rec.getReadName());
              continue;
            }
          }
          writer.addAlignment(rec);
          writeProgressLogger.record(rec);
        }
        tileRecord.setBarcodeState(barcode,TileBarcodeProcessingState.WRITTEN);
        findAndEnqueueWorkOrSignalCompletion();
      }
 catch (      RuntimeException e) {
        parentThread.interrupt();
        throw e;
      }
    }
  }
;
}

Fixed version (ground truth):
/** 
 * Returns a PriorityRunnable that encapsulates the work involved with writing the provided tileRecord's data for the given barcode to disk.
 * @param tile       The tile from which the record was read
 * @param tileRecord The processing record associated with the tile
 * @param barcode    The barcode whose data within the tileRecord is to be written
 * @return The runnable that upon invocation writes the barcode's data from the tileRecord to disk
 */
private PriorityRunnable newBarcodeWorkInstance(final Tile tile,final TileProcessingRecord tileRecord,final String barcode){
  return new PriorityRunnable(){
    @Override public void run(){
      try {
        final SortingCollection<SAMRecord> records=tileRecord.getBarcodeRecords().get(barcode);
        final SAMFileWriter writer=barcodeSamWriterMap.get(barcode);
        log.debug(String.format("String_Node_Str",tile.getNumber(),barcode));
        final PeekIterator<SAMRecord> it=new PeekIterator<SAMRecord>(records.iterator());
        while (it.hasNext()) {
          final SAMRecord rec=it.next();
          if (it.hasNext()) {
            final SAMRecord lookAhead=it.peek();
            if (!rec.getReadUnmappedFlag() || !lookAhead.getReadUnmappedFlag()) {
              throw new IllegalStateException("String_Node_Str");
            }
            if (samRecordQueryNameComparator.compare(rec,lookAhead) == 0) {
              it.next();
              log.info("String_Node_Str" + rec.getReadName());
              continue;
            }
          }
          writer.addAlignment(rec);
          writeProgressLogger.record(rec);
        }
        tileRecord.setBarcodeState(barcode,TileBarcodeProcessingState.WRITTEN);
        findAndEnqueueWorkOrSignalCompletion();
      }
 catch (      RuntimeException e) {
        parentThread.interrupt();
        throw e;
      }
catch (      Error e) {
        parentThread.interrupt();
        throw e;
      }
    }
  }
;
}