Program: 30669
Project: 30669
Buggy source:
protected BAMIndexContent query(final int referenceSequence,final int startPos,final int endPos){
  if (mFileBuffer == null)   throw new SAMException("String_Node_Str");
  seek(4);
  List<Bin> bins=null;
  LinearIndex linearIndex=null;
  final int sequenceCount=readInteger();
  if (referenceSequence >= sequenceCount) {
    return null;
  }
  final BitSet regionBins=regionToBins(startPos,endPos);
  if (regionBins == null) {
    return null;
  }
  skipToSequence(referenceSequence);
  final int binCount=readInteger();
  bins=new ArrayList<Bin>(binCount);
  for (int binNumber=0; binNumber < binCount; binNumber++) {
    List<Chunk> chunks=new ArrayList<Chunk>();
    final int indexBin=readInteger();
    final int nChunks=readInteger();
    if (regionBins.get(indexBin) || indexBin == MAX_BINS) {
      for (int ci=0; ci < nChunks; ci++) {
        final long chunkBegin=readLong();
        final long chunkEnd=readLong();
        chunks.add(new Chunk(chunkBegin,chunkEnd));
      }
    }
 else {
      skipBytes(16 * nChunks);
    }
    Bin bin=new Bin(referenceSequence,indexBin);
    bin.setChunkList(chunks);
    bins.add(bin);
  }
  Collections.sort(bins);
  final int nLinearBins=readInteger();
  final int regionLinearBinStart=LinearIndex.convertToLinearIndexOffset(startPos);
  final int regionLinearBinStop=LinearIndex.convertToLinearIndexOffset(endPos) > 0 ? LinearIndex.convertToLinearIndexOffset(endPos) : nLinearBins - 1;
  long[] linearIndexEntries=new long[0];
  if (regionLinearBinStart < nLinearBins) {
    linearIndexEntries=new long[regionLinearBinStop - regionLinearBinStart + 1];
    skipBytes(8 * regionLinearBinStart);
    for (int linearBin=regionLinearBinStart; linearBin <= regionLinearBinStop && linearBin <= nLinearBins - 1; linearBin++)     linearIndexEntries[linearBin - regionLinearBinStart]=readLong();
  }
  linearIndex=new LinearIndex(referenceSequence,regionLinearBinStart,linearIndexEntries);
  return new BAMIndexContent(referenceSequence,bins,linearIndex);
}

Fixed version (ground truth):
protected BAMIndexContent query(final int referenceSequence,final int startPos,final int endPos){
  if (mFileBuffer == null)   throw new SAMException("String_Node_Str");
  seek(4);
  List<Bin> bins=null;
  LinearIndex linearIndex=null;
  final int sequenceCount=readInteger();
  if (referenceSequence >= sequenceCount) {
    return null;
  }
  final BitSet regionBins=regionToBins(startPos,endPos);
  if (regionBins == null) {
    return null;
  }
  skipToSequence(referenceSequence);
  final int binCount=readInteger();
  bins=new ArrayList<Bin>(binCount);
  for (int binNumber=0; binNumber < binCount; binNumber++) {
    List<Chunk> chunks=new ArrayList<Chunk>();
    final int indexBin=readInteger();
    final int nChunks=readInteger();
    if (regionBins.get(indexBin) || indexBin == MAX_BINS) {
      for (int ci=0; ci < nChunks; ci++) {
        final long chunkBegin=readLong();
        final long chunkEnd=readLong();
        chunks.add(new Chunk(chunkBegin,chunkEnd));
      }
    }
 else {
      skipBytes(16 * nChunks);
    }
    Bin bin=new Bin(referenceSequence,indexBin);
    bin.setChunkList(chunks);
    bins.add(bin);
  }
  Collections.sort(bins);
  final int nLinearBins=readInteger();
  final int regionLinearBinStart=LinearIndex.convertToLinearIndexOffset(startPos);
  final int regionLinearBinStop=LinearIndex.convertToLinearIndexOffset(endPos) > 0 ? LinearIndex.convertToLinearIndexOffset(endPos) : nLinearBins - 1;
  final int actualStop=Math.min(regionLinearBinStop,nLinearBins - 1);
  long[] linearIndexEntries=new long[0];
  if (regionLinearBinStart < nLinearBins) {
    linearIndexEntries=new long[actualStop - regionLinearBinStart + 1];
    skipBytes(8 * regionLinearBinStart);
    for (int linearBin=regionLinearBinStart; linearBin <= actualStop; linearBin++)     linearIndexEntries[linearBin - regionLinearBinStart]=readLong();
  }
  linearIndex=new LinearIndex(referenceSequence,regionLinearBinStart,linearIndexEntries);
  return new BAMIndexContent(referenceSequence,bins,linearIndex);
}