message: minor code cleanup for clarity
diff: @@ -2022,9 +2022,6 @@ void AlleleParser::updateAlignmentQueue(long int position,
  if (parameters.baseQualityCap != 0) {
  capBaseQuality(currentAlignment, parameters.baseQualityCap);
  }
  - // decomposes alignment into a set of alleles
  - // here we get the deque of alignments ending at this alignment's end position
  - deque<RegisteredAlignment>& rq = registeredAlignments[currentAlignment.ENDPOSITION];
  // do we exceed coverage anywhere?
  // do we touch anything where we had exceeded coverage?
  // if so skip this read, and mark and remove processed alignments and registered alleles overlapping the coverage capped position
  @@ -2047,7 +2044,9 @@ void AlleleParser::updateAlignmentQueue(long int position,
  }
  }
  }
  -
  + // decomposes alignment into a set of alleles
  + // here we get the deque of alignments ending at this alignment's end position
  + deque<RegisteredAlignment>& rq = registeredAlignments[currentAlignment.ENDPOSITION];
  //cerr << "parameters capcoverage " << parameters.capCoverage << " " << rq.size() << endl;
  if (considerAlignment) {
  // and insert the registered alignment into that deque
  