Program: 50304
Project: 50304
Buggy source:
/** 
 * Perform the concatenation.
 * @throws java.io.IOException
 */
@Override public void execute() throws IOException {
  final String[] basenames=AlignmentReaderImpl.getBasenames(inputFilenames);
  final boolean allSorted=ConcatenateAlignmentMode.isAllSorted(basenames);
  if (!allSorted) {
    System.out.println("String_Node_Str");
    System.exit(10);
  }
  if (readIndexStats != null) {
    int readerIndex=0;
    for (    String basename : basenames) {
      boolean found=false;
      for (      ReadIndexStats stat : readIndexStats) {
        if (FilenameUtils.getBaseName(basename).equals(stat.basename)) {
          stat.readerIndex=readerIndex;
          found=true;
        }
      }
      if (!found) {
        System.err.printf("String_Node_Str",basename);
        System.err.flush();
      }
      readerIndex++;
    }
    Collections.sort(readIndexStats,new Comparator<ReadIndexStats>(){
      public int compare(      ReadIndexStats readIndexStats,      ReadIndexStats readIndexStatsFirst){
        return readIndexStats.readerIndex - readIndexStatsFirst.readerIndex;
      }
    }
);
    final int sampleToGroupAssociationNumber=this.deCalculator.getSampleToGroupMap().keySet().size();
    numberOfReadIndices=new int[inputFilenames.length];
    ObjectSet<ReadIndexStats> toRemove=new ObjectArraySet<ReadIndexStats>();
    for (    ReadIndexStats stat : readIndexStats) {
      if (stat.readerIndex == -1) {
        toRemove.add(stat);
        continue;
      }
      numberOfReadIndices[stat.readerIndex]=Math.max(numberOfReadIndices[stat.readerIndex],stat.countReferenceBases.length);
    }
    readIndexStats.removeAll(toRemove);
  }
  sortedPositionIterator.allocateStorage(basenames.length,numberOfGroups);
  sortedPositionIterator.initialize(this,outputInfo,genotypeFilters);
  sortedPositionIterator.setAlignmentReaderFactory(new NonAmbiguousAlignmentReaderFactory());
  sortedPositionIterator.setAlignmentProcessorFactory(realignmentFactory);
  sortedPositionIterator.setOverrideReferenceWithGenome(overrideReferenceWithGenome);
  sortedPositionIterator.setMaxThreshold(maxThresholdPerSite);
  sortedPositionIterator.iterate(basenames);
  sortedPositionIterator.finish();
}

Fixed version (ground truth):
/** 
 * Perform the concatenation.
 * @throws java.io.IOException
 */
@Override public void execute() throws IOException {
  final String[] basenames=AlignmentReaderImpl.getBasenames(inputFilenames);
  final boolean allSorted=ConcatenateAlignmentMode.isAllSorted(basenames);
  if (!allSorted) {
    System.out.println("String_Node_Str");
    System.exit(10);
  }
  if (readIndexStats != null) {
    int readerIndex=0;
    for (    String basename : basenames) {
      boolean found=false;
      for (      ReadIndexStats stat : readIndexStats) {
        if (FilenameUtils.getName(basename).equals(stat.basename)) {
          stat.readerIndex=readerIndex;
          found=true;
        }
      }
      if (!found) {
        System.err.printf("String_Node_Str",basename);
        System.err.flush();
      }
      readerIndex++;
    }
    Collections.sort(readIndexStats,new Comparator<ReadIndexStats>(){
      public int compare(      ReadIndexStats readIndexStats,      ReadIndexStats readIndexStatsFirst){
        return readIndexStats.readerIndex - readIndexStatsFirst.readerIndex;
      }
    }
);
    final int sampleToGroupAssociationNumber=this.deCalculator.getSampleToGroupMap().keySet().size();
    numberOfReadIndices=new int[inputFilenames.length];
    ObjectSet<ReadIndexStats> toRemove=new ObjectArraySet<ReadIndexStats>();
    for (    ReadIndexStats stat : readIndexStats) {
      if (stat.readerIndex == -1) {
        toRemove.add(stat);
        continue;
      }
      numberOfReadIndices[stat.readerIndex]=Math.max(numberOfReadIndices[stat.readerIndex],stat.countReferenceBases.length);
    }
    readIndexStats.removeAll(toRemove);
  }
  sortedPositionIterator.allocateStorage(basenames.length,numberOfGroups);
  sortedPositionIterator.initialize(this,outputInfo,genotypeFilters);
  sortedPositionIterator.setAlignmentReaderFactory(new NonAmbiguousAlignmentReaderFactory());
  sortedPositionIterator.setAlignmentProcessorFactory(realignmentFactory);
  sortedPositionIterator.setOverrideReferenceWithGenome(overrideReferenceWithGenome);
  sortedPositionIterator.setMaxThreshold(maxThresholdPerSite);
  sortedPositionIterator.iterate(basenames);
  sortedPositionIterator.finish();
}