/*Want to access P-value, I statistic, and name of test.
*
* void gene_accumulate_assoc( VariantGroup & vars , void *p ){
Py_geneassocGroup geneassocgroup;
std::vector<Py_test> tests;
for( int i = 0; i < )
}*/
void group_accumulate_func( VariantGroup &v, void *p ){
//Variant Group
Py_variantGroup vargroup;
vargroup.NV = v.n_variants();
vargroup.SIZE = v.size();
vargroup.COORD = v.coordinate();
vargroup.SPAN = v.span();
vargroup.MIDPOS = v.midposition();
vargroup.NAME = v.name();
vargroup.NIND = v.n_individuals();
std::vector<Py_variant> vars;
for(int i = 0; i < v.n_variants(); i++){
// Add new variant to the vector of variant groups.
Variant vn = v.var(i);
Py_variant var;
var.CHR = vn.chromosome();
var.BP1 = vn.position();
var.BP2 = vn.stop();
var.ID = vn.name();
var.NS = vn.n_samples();
// Sample variant
SampleVariant &sv = vn.sample(-1);
Py_sample_variant svar;
svar.FSET = sv.fileset();
svar.REF = sv.reference();
svar.ALT = sv.alternate();
svar.QUAL = sv.quality();
// Genotype
Py_genotype py_geno;
std::vector<int> gt;
int nind = vn.size(-1);
for (int i = 0; i < nind; i++) {
Genotype* geno = vn.genotype(-1, i);
if (geno->more() || geno->null()) {
gt.push_back(-1); // Code NA as -1
} else {
gt.push_back(geno->allele_count());
}
}
py_geno.GT = gt;
svar.GENO = py_geno;
var.CON = svar;
vars.push_back(var);
}
vargroup.VARS = vars;
std::vector<Py_variantGroup>* d = (std::vector<Py_variantGroup>*)p;
d->push_back(vargroup);
}
void accumulate_func(Variant &v, void *p) {
// Variant
Py_variant var;
var.CHR = v.chromosome();
var.BP1 = v.position();
var.BP2 = v.stop();
var.ID = v.name();
var.NS = v.n_samples();
// Sample variant
SampleVariant &sv = v.sample(-1);
Py_sample_variant svar;
svar.FSET = sv.fileset();
svar.REF = sv.reference();
svar.ALT = sv.alternate();
svar.QUAL = sv.quality();
// Genotype
Py_genotype py_geno;
std::vector<int> gt;
int nind = v.size(-1);
for (int i = 0; i < nind; i++) {
Genotype* geno = v.genotype(-1, i);
if (geno->more() || geno->null()) {
gt.push_back(-1); // Code NA as -1
} else {
gt.push_back(geno->allele_count());
}
}
py_geno.GT = gt;
svar.GENO = py_geno;
var.CON = svar;
// Add new variant to the vector of variants
std::vector<Py_variant>* d = (std::vector<Py_variant>*)p;
d->push_back(var);
}
