Program: 50359
Project: 50359
Buggy source:
private void decompressBits(InputBitStream bitInput,final int numEntriesInChunk) throws IOException {
  multiplicityFieldsAllMissing=bitInput.readBit() == 1;
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,deltaPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,deltaTargetIndices);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,mappingQualities);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,matchingReverseStrand);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,numberOfIndels);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,numberOfMismatches);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryAlignedLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,targetAlignedLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,fragmentIndices);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,variationCount);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,fromLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,toLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varReadIndex);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varFromTo);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varQuals);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varHasToQuals);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,multiplicities);
  pairLinks.read(numEntriesInChunk,bitInput);
  forwardSpliceLinks.read(numEntriesInChunk,bitInput);
  backwardSpliceLinks.read(numEntriesInChunk,bitInput);
  decodeQueryIndices("String_Node_Str",numEntriesInChunk,bitInput,queryIndices);
}

Fixed version (ground truth):
private void decompressBits(InputBitStream bitInput,final int numEntriesInChunk) throws IOException {
  multiplicityFieldsAllMissing=bitInput.readBit() == 1;
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,deltaPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,deltaTargetIndices);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,mappingQualities);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,matchingReverseStrand);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,numberOfIndels);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,numberOfMismatches);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryAlignedLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,targetAlignedLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,queryPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,fragmentIndices);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,variationCount);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varPositions);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,fromLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,toLengths);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varReadIndex);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varFromTo);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varQuals);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,varToQualLength);
  decodeArithmetic("String_Node_Str",numEntriesInChunk,bitInput,multiplicities);
  pairLinks.read(numEntriesInChunk,bitInput);
  forwardSpliceLinks.read(numEntriesInChunk,bitInput);
  backwardSpliceLinks.read(numEntriesInChunk,bitInput);
  decodeQueryIndices("String_Node_Str",numEntriesInChunk,bitInput,queryIndices);
}