bool hasAmbiguous(Variant & variant) {
for (uint allele_idx = 0; allele_idx < variant.numAlls(); allele_idx++) {
if (hasAmbiguous(variant.allele(allele_idx))) {
return true;
}
}
return false;
}
vector<uint> getCalledAlleleIdxsSorted(Variant & var, const float min_acp) {
vector<uint> called_allele_idxs;
for (uint allele_idx = 0; allele_idx < var.numAlls(); allele_idx++) {
if (isAlleleCalled(var.allele(allele_idx), min_acp)) {
called_allele_idxs.push_back(allele_idx);
}
}
return called_allele_idxs;
}
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;
}
vector<uint> getNonZeroProbAlleleIdxsSorted(Variant & var) {
vector<uint> non_zero_prob_allele_idxs;
for (uint allele_idx = 0; allele_idx < var.numAlls(); allele_idx++) {
auto acp_value = var.allele(allele_idx).info().getValue<float>("ACP");
if (acp_value.second) {
if (!(Utils::floatCompare(acp_value.first, 0))) {
non_zero_prob_allele_idxs.push_back(allele_idx);
}
}
}
return non_zero_prob_allele_idxs;
}
Trio::Trio(Variant & cur_var, const TrioInfo & trio_info) {
father = cur_var.getSample(trio_info.father);
mother = cur_var.getSample(trio_info.mother);
child = cur_var.getSample(trio_info.child);
is_filtered = ((father.callStatus() == Sample::CallStatus::Missing) or (mother.callStatus() == Sample::CallStatus::Missing) or (child.callStatus() == Sample::CallStatus::Missing));
is_diploid = ((father.ploidy() == Sample::Ploidy::Diploid) and (mother.ploidy() == Sample::Ploidy::Diploid) and (child.ploidy() == Sample::Ploidy::Diploid));
assert((father.ploidy() != Sample::Ploidy::Zeroploid) or (mother.ploidy() != Sample::Ploidy::Zeroploid) or (child.ploidy() != Sample::Ploidy::Zeroploid));
is_informative = true;
is_concordant = false;
is_exclusively_child_heterozygote = true;
is_parents_bi_allelelic_heterozygote = false;
is_reference_call = true;
has_called_missing = false;
if (!is_filtered) {
auto father_genotype = father.genotypeEstimate();
auto mother_genotype = mother.genotypeEstimate();
auto child_genotype = child.genotypeEstimate();
bool first_child_allele_in_father = false;
bool second_child_allele_in_father = false;
bool first_child_allele_in_mother = false;
bool second_child_allele_in_mother = false;
if (child_genotype.size() > 0) {
assert(child.ploidy() != Sample::Ploidy::Zeroploid);
first_child_allele_in_father = (find(father_genotype.begin(), father_genotype.end(), child_genotype.front()) != father_genotype.end());
second_child_allele_in_father = (find(father_genotype.begin(), father_genotype.end(), child_genotype.back()) != father_genotype.end());
first_child_allele_in_mother = (find(mother_genotype.begin(), mother_genotype.end(), child_genotype.front()) != mother_genotype.end());
second_child_allele_in_mother = (find(mother_genotype.begin(), mother_genotype.end(), child_genotype.back()) != mother_genotype.end());
}
if (cur_var.chrom() == "chrX") {
if (!is_diploid) {
assert(father.ploidy() == Sample::Ploidy::Haploid);
assert(father_genotype.size() == 1);
assert(mother.ploidy() == Sample::Ploidy::Diploid);
assert(mother_genotype.size() == 2);
if (child.ploidy() == Sample::Ploidy::Diploid) {
assert(child_genotype.size() == 2);
is_concordant = ((first_child_allele_in_father and second_child_allele_in_mother) or (second_child_allele_in_father and first_child_allele_in_mother));
} else {
assert(child.ploidy() == Sample::Ploidy::Haploid);
assert(child_genotype.size() == 1);
assert(first_child_allele_in_mother == second_child_allele_in_mother);
is_concordant = first_child_allele_in_mother;
}
} else {
is_informative = false;
is_concordant = false;
}
} else if (cur_var.chrom() == "chrY") {
if (!is_diploid) {
assert(father.ploidy() == Sample::Ploidy::Haploid);
assert(father_genotype.size() == 1);
assert(mother.ploidy() == Sample::Ploidy::Zeroploid);
assert(mother_genotype.size() == 0);
assert(!first_child_allele_in_mother and !second_child_allele_in_mother);
assert(first_child_allele_in_father == second_child_allele_in_father);
if (child.ploidy() == Sample::Ploidy::Haploid) {
assert(child_genotype.size() == 1);
is_concordant = first_child_allele_in_father;
} else {
assert(child.ploidy() == Sample::Ploidy::Zeroploid);
assert(child_genotype.size() == 0);
assert(!first_child_allele_in_father);
is_informative = false;
is_concordant = false;
}
} else {
is_informative = false;
is_concordant = false;
}
} else {
assert(is_diploid);
assert(father_genotype.size() == 2);
assert(mother_genotype.size() == 2);
assert(child_genotype.size() == 2);
is_concordant = ((first_child_allele_in_father and second_child_allele_in_mother) or (second_child_allele_in_father and first_child_allele_in_mother));
if (cur_var.numAlls() == 2) {
if ((father_genotype.front() != father_genotype.back()) and (mother_genotype.front() != mother_genotype.back())) {
is_parents_bi_allelelic_heterozygote = true;
}
}
}
if (child.ploidy() != Sample::Ploidy::Diploid) {
is_exclusively_child_heterozygote = false;
} else if ((father.ploidy() == Sample::Ploidy::Zeroploid) or (mother.ploidy() == Sample::Ploidy::Zeroploid)) {
is_exclusively_child_heterozygote = false;
} else if ((father_genotype.front() != father_genotype.back()) or (mother_genotype.front() != mother_genotype.back())) {
is_exclusively_child_heterozygote = false;
} else if (child_genotype.front() == child_genotype.back()) {
is_exclusively_child_heterozygote = false;
}
auto all_called_alleles = father_genotype;
all_called_alleles.insert(all_called_alleles.end(), mother_genotype.begin(), mother_genotype.end());
all_called_alleles.insert(all_called_alleles.end(), child_genotype.begin(), child_genotype.end());
assert(all_called_alleles.size() > 0);
for (auto &allele_idx: all_called_alleles) {
if (cur_var.allele(allele_idx).isMissing()) {
has_called_missing = true;
}
if (allele_idx > 0) {
is_reference_call = false;
}
}
de_novo_event.first = false;
if (is_diploid and !is_concordant and is_exclusively_child_heterozygote and !has_called_missing) {
uint ancestral_allele_idx = 0;
uint de_novo_allele_idx = 0;
if ((!first_child_allele_in_father and !first_child_allele_in_mother) and (second_child_allele_in_father or second_child_allele_in_mother)) {
de_novo_allele_idx = child_genotype.front();
} else if ((!second_child_allele_in_father and !second_child_allele_in_mother) and (first_child_allele_in_father or first_child_allele_in_mother)) {
de_novo_allele_idx = child_genotype.back();
}
if (de_novo_allele_idx == father_genotype.front()) {
ancestral_allele_idx = mother_genotype.front();
} else {
ancestral_allele_idx = father_genotype.front();
}
if (de_novo_allele_idx > 0) {
assert(de_novo_allele_idx != ancestral_allele_idx);
de_novo_event.first = true;
de_novo_event.second.child_id = trio_info.child;
de_novo_event.second.ancestral_allele_idx = ancestral_allele_idx;
de_novo_event.second.de_novo_allele_idx = de_novo_allele_idx;
}
}
}
}
