message: force quality to be 0 when no quality string given
  In response to
diff: @@ -1317,6 +1317,13 @@ RegisteredAlignment& AlleleParser::registerAlignment(BAMALIGN& alignment, Regist
  string rDna = alignment.QUERYBASES;
  string rQual = alignment.QUALITIES;
  + if (qualityChar2LongDouble(rQual.at(0)) == -1) {
  + // force rQual to be 0
  + char q0 = qualityInt2Char(0);
  + for (size_t i = 0; i < rQual.size(); ++i) {
  + rQual[i] = q0;
  + }
  + }
  int rp = 0; // read position, 0-based relative to read
  int csp = currentSequencePosition(alignment); // current sequence position, 0-based relative to currentSequence
  int sp = alignment.POSITION; // sequence position
  @@ -1979,12 +1986,8 @@ void AlleleParser::updateAlignmentQueue(long int position,
  }
  // skip alignments which are non-primary
  -#ifdef HAVE_BAMTOOLS
  - if (!currentAlignment.IsPrimaryAlignment()) {
  -#else
  if (currentAlignment.SecondaryFlag()) {
  -#endif
  - //DEBUG("skipping alignment " << currentAlignment.Name << " because it is not marked primary");
  + DEBUG("skipping alignment " << currentAlignment.QNAME << " because it is not marked primary");
  continue;
  }
  @@ -3341,12 +3344,15 @@ void AlleleParser::buildHaplotypeAlleles(
  groupAlleles(samples, alleleGroups);
  /*
  + if (parameters.debug) {
  + DEBUG("after re-grouping alleles");
  for (Samples::iterator s = samples.begin(); s != samples.end(); ++s) {
  cerr << s->first << endl;
  for (Sample::iterator t = s->second.begin(); t != s->second.end(); ++t) {
  cerr << t->first << " " << t->second << endl << endl;
  }
  }
  + }
  */
  Allele refAllele = genotypeAllele(ALLELE_REFERENCE,
  