message: Ignore case when input allele is bigger than ref
diff: @@ -3990,10 +3990,9 @@ vector<Allele> AlleleParser::genotypeAlleles(
  }
  }
  if (!alreadyPresent) {
  - if (allele.position == currentPosition && allele.referenceLength == haplotypeLength) {
  + if (allele.position <= currentPosition && allele.referenceLength >= haplotypeLength) {
  resultAlleles.push_back(allele);
  } else {
  - assert(currentPosition <= allele.position && haplotypeLength >= allele.referenceLength);
  string altseq = "";
  string cigar = "";
  long int extend_left = allele.position - currentPosition;
  