message: can we get away without sorting and removing "non-unique" alleles?
diff: @@ -2881,8 +2881,6 @@ bool AlleleParser::toNextPosition(void) {
  // remove past registered alleles
  DEBUG2("marking previous alleles as processed and removing from registered alleles");
  removePreviousAlleles(registeredAlleles, currentPosition);
  - sort(registeredAlleles.begin(), registeredAlleles.end());
  - registeredAlleles.erase(unique(registeredAlleles.begin(), registeredAlleles.end()), registeredAlleles.end());
  // if we have alignments which ended at the previous base, erase them and their alleles
  DEBUG2("erasing old registered alignments");
  