bool hasAnnotatedAlternativeAllele(Variant & variant) {
for (uint alt_idx = 0; alt_idx < variant.numAlts(); alt_idx++) {
if (isAlleleAnnotated(variant.alt(alt_idx))) {
return true;
}
}
return false;
}
bool hasMissing(Variant & variant) {
assert(!(variant.allele(0).isMissing()));
for (uint alt_idx = 0; alt_idx < variant.numAlts(); alt_idx++) {
if (variant.alt(alt_idx).isMissing()) {
return true;
}
}
return false;
}
string variantType(Variant & variant) {
assert(variant.numAlts() > hasMissing(variant));
if (variant.numAlts() > (1 + static_cast<uint>(hasMissing(variant)))) {
return "Multi";
}
auto cur_type = alleleAttributes(variant.alt(0), variant.ref());
assert(cur_type.type != Type::Reference);
assert(cur_type.type != Type::Missing);
return cur_type.typeStr();
}
bool hasRepeat(Variant & variant) {
for (uint alt_idx = 0; alt_idx < variant.numAlts(); alt_idx++) {
auto rma_value = variant.alt(alt_idx).info().getValue<string>("RMA");
if (rma_value.second) {
if (rma_value.first != ".") {
return true;
}
}
}
return false;
}