// Entry point for variant classification
bool AlleleIdentity::getVariantType(
const string _altAllele,
const LocalReferenceContext &reference_context,
const TIonMotifSet & ErrorMotifs,
const ClassifyFilters &filter_variant,
const ReferenceReader &ref_reader,
int chr_idx) {
altAllele = _altAllele;
bool is_ok = reference_context.context_detected;
if ((reference_context.position0 + (long)altAllele.length()) > ref_reader.chr_size(chr_idx)) {
is_ok = false;
}
// We should now be guaranteed a valid variant position in here
if (is_ok) {
is_ok = CharacterizeVariantStatus(reference_context, ref_reader, chr_idx);
PredictSequenceMotifSSE(reference_context, ErrorMotifs, ref_reader, chr_idx);
}
is_ok = is_ok and CheckValidAltAllele(reference_context);
if (!is_ok) {
status.isProblematicAllele = true;
filterReasons.push_back("BADCANDIDATE");
}
return(is_ok);
}
// Entry point for variant classification
bool AlleleIdentity::getVariantType(
string _altAllele,
LocalReferenceContext &reference_context,
const string & local_contig_sequence,
TIonMotifSet & ErrorMotifs,
ClassifyFilters &filter_variant) {
altAllele = _altAllele;
bool is_ok = reference_context.context_detected;
// We should now be guaranteed a valid variant position in here
if (is_ok) {
is_ok = CharacterizeVariantStatus(reference_context, filter_variant.min_hp_for_overcall);
PredictSequenceMotifSSE(reference_context, local_contig_sequence, ErrorMotifs);
// Just confusing -> refactor away
ModifyStartPosForAllele(reference_context.position0 + 1);
}
is_ok = is_ok and CheckValidAltAllele(reference_context);
if (!is_ok) {
status.isNoCallVariant = true;
filterReason += ",NOCALLxBADCANDIDATE";
}
return(is_ok);
}
