void RemoveFilteredAlleles(vcf::Variant &candidate_variant, vector<int> &filtered_alleles_index) {
//now that all possible alt. alleles are evaluated decide on which allele is most likely and remove any that
//that does'nt pass score threshold. Determine Genotype based on alleles that have evidence.
candidate_variant.updateAlleleIndexes();
string my_healing_glow = "HEALED";
vector<string> originalAltAlleles = candidate_variant.alt;
if (originalAltAlleles.size() > 1 &&
originalAltAlleles.size() > filtered_alleles_index.size() //remove only when number of alleles more than number of filtered alleles
&& !candidate_variant.isHotSpot) { //dont remove alleles if it is a HOT SPOT position as alleles might have been provided by the user.
//remove filtered alleles with no support
string altStr;
int index;
for (size_t i = 0; i <filtered_alleles_index.size(); i++) {
index = filtered_alleles_index[i];
//generate allele index before removing alleles
altStr = originalAltAlleles[index];
// specify what the alleles removed are
//my_healing_glow = "HEALED" + altStr;
//altStr = (*candidate_variant)->alt[index];
// Note: need to update index for adjustments
//AdjustFDPForRemovedAlleles(candidate_variant, index, sample_name);
//cout << "Removed Fitered allele: index = " << index << " allele = " << altStr << endl;
// @TODO: removeAlt wrecks the genotype as well
// fix so we don't remove genotype components.
candidate_variant.removeAlt(altStr);
candidate_variant.updateAlleleIndexes();
// if we are deleting alleles, indicate data potentially damaged at this location
AddFilterReason(candidate_variant, my_healing_glow);
}
}
}
void DoStepsForNoData(VariantCandidate& candidate_variant, const string& sample_name, int sample_index, bool use_molecular_tag, string my_reason){
//cerr << "Nonfatal: No reads found for " << candidate_variant.variant.sequenceName << "\t" << my_ensemble.multiallele_window_start << endl;
NullFilterReason(candidate_variant.variant, sample_name);
if (my_reason.empty()){
my_reason = "NODATA";
}
AddFilterReason(candidate_variant.variant, my_reason, sample_name);
SetFilteredStatus(candidate_variant.variant, true);
candidate_variant.variant.samples[sample_name]["GT"] = {"./."};
}
void NullFilterReason(vcf::Variant &candidate_variant) {
ClearVal(candidate_variant, "FR");
string my_null_filter = ".";
AddFilterReason(candidate_variant, my_null_filter);
}
