message: clarify that alignments mapping past the end of contigs indicates a potential problem with the input
diff: @@ -1454,13 +1454,11 @@ RegisteredAlignment& AlleleParser::registerAlignment(BAMALIGN& alignment, Regist
  try {
  sb = currentSequence.at(csp);
  } catch (std::out_of_range outOfRange) {
  - cerr << "Exception: Unable to read reference sequence base past end of current cached sequence." << endl
  - << currentSequenceName << ":" << (long unsigned int) currentPosition + 1 << endl
  - << alignment.POSITION << "-" << alignment.ENDPOSITION << endl
  - //<< "alignment: " << alignment.AlignedBases << endl
  - << "currentSequence: " << currentSequence << endl
  - << "currentSequence matching: " << currentSequence.substr(csp, alignment.ALIGNEDBASES) << endl;
  - //abort();
  + cerr << "Exception: Alignment reports a match past the end of the current reference sequence." << endl
  + << "This suggests alignment corruption or a mismatch between this reference and the alignments." << endl
  + << "Are you sure that you are calling against the same reference you aligned to?" << endl
  + << "Sequence: " << currentSequenceName << ":" << (long unsigned int) currentPosition + 1 << endl
  + << "Alignment: " << alignment.QNAME << " @ " << alignment.POSITION << "-" << alignment.ENDPOSITION << endl;
  break;
  }
  