AlleleAttributes alleleAttributes(Allele & main_allele, Allele & reference_allele) {
assert(!(main_allele.seq().empty()));
assert(!(reference_allele.seq().empty()));
assert(!(reference_allele.isMissing()));
if (main_allele.isMissing()) {
return AlleleAttributes(Type::Missing, 0, 0, 0);
}
if (main_allele == reference_allele) {
return AlleleAttributes(Type::Reference, main_allele.seq().size(), count(main_allele.seq().begin(), main_allele.seq().end(), 'N'), 0);
}
Allele trimmed_main_allele = main_allele;
Allele trimmed_reference_allele = reference_allele;
fullTrimAllelePair(&trimmed_main_allele, &trimmed_reference_allele);
assert(!(trimmed_main_allele.seq().empty()) or !(trimmed_reference_allele.seq().empty()));
uint trimmed_main_allele_length = trimmed_main_allele.seq().size();
uint trimmed_reference_allele_length = trimmed_reference_allele.seq().size();
uint trimmed_main_allele_num_ambiguous = count(trimmed_main_allele.seq().begin(), trimmed_main_allele.seq().end(), 'N');
if (trimmed_main_allele_length == trimmed_reference_allele_length) {
auto allele_type = Type::Complex;
if (trimmed_main_allele_length == 1) {
allele_type = Type::SNP;
} else if (isInversion(trimmed_main_allele, trimmed_reference_allele, 0.95, 10)) {
allele_type = Type::Inversion;
}
return AlleleAttributes(allele_type, trimmed_main_allele_length, trimmed_main_allele_num_ambiguous, 0);
} else {
auto allele_type = Type::Complex;
if (trimmed_main_allele_length == 0) {
allele_type = Type::Deletion;
} else if (trimmed_reference_allele_length == 0) {
allele_type = Type::Insertion;
}
return AlleleAttributes(allele_type, trimmed_main_allele_length, trimmed_main_allele_num_ambiguous, trimmed_main_allele_length - trimmed_reference_allele_length);
}
}
string getAlleleStringAttribute(Allele & allele, const string attribute) {
auto att_value = allele.info().getValue<string>(attribute);
if (att_value.second) {
if (att_value.first == ".") {
return "NoValue";
} else {
assert(!(allele.isMissing()));
return att_value.first;
}
} else {
return "Reference";
}
}