void AdjustFDPForRemovedAlleles(vcf::Variant &candidate_variant, int filtered_allele_index, string sampleName)
{
// first do the "info" tag as it is easier to find
map<string, vector<string> >::iterator it;
int total_depth=0;
it = candidate_variant.info.find("FDP");
if (it != candidate_variant.info.end())
total_depth = atoi(candidate_variant.info["FDP"][0].c_str()); // or is this current sample ident?
int allele_depth = 0;
it = candidate_variant.info.find("FAO");
if (it != candidate_variant.info.end())
allele_depth = atoi(candidate_variant.info["FAO"][filtered_allele_index].c_str());
total_depth -= allele_depth;
if (total_depth<0)
total_depth = 0; // how can this happen?
ClearVal(candidate_variant, "FDP");
candidate_variant.info["FDP"].push_back(convertToString(total_depth));
if (!sampleName.empty()) {
map<string, vector<string> >& sampleOutput = candidate_variant.samples[sampleName];
sampleOutput["FDP"].clear();
sampleOutput["FDP"].push_back(convertToString(total_depth));
}
}
BOOL CParmFindOneDlg::SetValues()
{
if (m_pRun->SetValues(this)) {
UpdateVal();
return TRUE;
} else {
ClearVal();
return FALSE;
}
}
void NullFilterReason(vcf::Variant &candidate_variant) {
ClearVal(candidate_variant, "FR");
string my_null_filter = ".";
AddFilterReason(candidate_variant, my_null_filter);
}
//clear all the info tags, in case of a HotSpot VCF react Info tags might contain prior values
void clearInfoTags(vcf::Variant &var) {
map<string, vector<string> >::iterator it;
it = var.info.find("RO");
if (it != var.info.end())
var.info["RO"].clear();
it = var.info.find("AO");
if (it != var.info.end())
var.info["AO"].clear();
it = var.info.find("SAF");
if (it != var.info.end())
var.info["SAF"].clear();
it = var.info.find("SAR");
if (it != var.info.end())
var.info["SAR"].clear();
it = var.info.find("SRF");
if (it != var.info.end())
var.info["SRF"].clear();
it = var.info.find("SRR");
if (it != var.info.end())
var.info["SRR"].clear();
it = var.info.find("DP");
if (it != var.info.end())
var.info["DP"].clear();
it = var.info.find("RBI");
if (it != var.info.end())
var.info["RBI"].clear();
it = var.info.find("HRUN");
if (it != var.info.end())
var.info["HRUN"].clear();
it = var.info.find("MLLD");
if (it != var.info.end())
var.info["MLLD"].clear();
//SSE compute
ClearVal(var,"SSSB");
ClearVal(var,"SSEN");
ClearVal(var,"SSEP");
it = var.info.find("STB");
if (it != var.info.end())
var.info["STB"].clear();
it = var.info.find("STBP");
if (it != var.info.end())
var.info["STBP"].clear();
it = var.info.find("PBP");
if (it != var.info.end())
var.info["PBP"].clear();
/* it = var.info.find("SXB");
if (it != var.info.end())
var.info["SXB"].clear();*/
ClearVal(var,"FDP");
ClearVal(var,"FRO");
ClearVal(var,"FAO");
//ClearVal(var,"JUNK");
ClearVal(var,"AF");
ClearVal(var,"FSRF");
ClearVal(var,"FSRR");
ClearVal(var,"FSAF");
ClearVal(var,"FSAR");
ClearVal(var,"FXX");
ClearVal(var,"QD");
}
