message: Bug fix: input allele is too short
diff: @@ -3990,7 +3990,36 @@ vector<Allele> AlleleParser::genotypeAlleles(
  }
  }
  if (!alreadyPresent) {
  + 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;
  + long int extend_right = currentPosition + haplotypeLength
  + - allele.position - allele.referenceLength;
  + if (extend_left > 0) {
  + altseq += currentSequence.substr(currentPosition - currentSequenceStart, extend_left);
  + cigar += convert(extend_left) + "M";
  + }
  + altseq += allele.alternateSequence;
  + cigar += allele.cigar;
  + if (extend_right > 0) {
  + altseq += currentSequence.substr(
  + allele.position + allele.referenceLength - currentSequenceStart, extend_right);
  + cigar += convert(extend_right) + "M";
  + }
  + Allele new_allele = genotypeAllele(allele.type,
  + altseq,
  + allele.length + extend_left + extend_right,
  + cigar,
  + haplotypeLength,
  + currentPosition,
  + allele.repeatRightBoundary);
  + DEBUG("Extending input allele " << allele << " -> " << new_allele);
  + resultAlleles.push_back(new_allele);
  + }
  }
  }
  }
  