message: optimized minDepth logic, and added format fields
diff: @@ -676,17 +676,15 @@ vcflib::Variant& Results::gvcf(
  var.format.push_back("DP");
  var.format.push_back("MIN_DP");
  var.format.push_back("QR");
  + var.format.push_back("RO");
  var.format.push_back("QA");
  + var.format.push_back("AO");
  NonCall total = nonCalls.aggregateAll();
  /* This resets min depth to zero if nonCalls is less than numSites. */
  - int minDepth = total.minDepth;
  -
  - if(numSites != total.nCount){
  - minDepth = 0;
  - }
  + int minDepth = (numSites != nc.count) ? 0 : nc.minDepth;
  var.info["DP"].push_back(convert((total.refCount+total.altCount) / numSites));
  var.info["MIN_DP"].push_back(convert(minDepth));
  @@ -711,16 +709,15 @@ vcflib::Variant& Results::gvcf(
  /* This resets min depth to zero if nonCalls is less than numSites. */
  - int minDepth = nc.minDepth;
  + int minDepth = (numSites != nc.count) ? 0 : nc.minDepth;
  - if(numSites != nc.nCount){
  - minDepth = 0;
  - }
  sampleOutput["DP"].push_back(convert((nc.refCount+nc.altCount) / numSites));
  sampleOutput["MIN_DP"].push_back(convert(minDepth));
  sampleOutput["QR"].push_back(convert(ln2phred(nc.reflnQ)));
  + sampleOutput["RO"].pushback(convert((nc.refCount/numSites));
  sampleOutput["QA"].push_back(convert(ln2phred(nc.altlnQ)));
  + sampleOutput["AO"].push_back(convert((nc.altCount/numsites));
  }
  return var;
  