//' @rdname is_het
//' @name is_het
//'
//'
//'
//' @export
// [[Rcpp::export]]
Rcpp::LogicalMatrix is_het(Rcpp::StringMatrix x,
Rcpp::LogicalVector na_is_false = true
){
// NA matrix to return in case of unexpected results.
// Rcpp::LogicalMatrix nam( 1, 1 );
// nam(0,0) = NA_LOGICAL;
// Initialize return data matrix.
Rcpp::LogicalMatrix hets( x.nrow(), x.ncol() );
hets.attr("dimnames") = x.attr("dimnames");
int i;
int j;
int k;
for( i=0; i<x.nrow(); i++){
for( j=0; j<x.ncol(); j++){
// Parse genotype string into alleles.
std::string my_string;
if( x(i,j) == NA_STRING ){
my_string = ".";
} else {
my_string = x(i,j);
}
std::vector < std::string > allele_vec;
// vcfRCommon::strsplit(my_string, allele_vec, my_split);
int unphased_as_na = 0; // 0 == FALSE
vcfRCommon::gtsplit( my_string, allele_vec, unphased_as_na );
// Rcpp::Rcout << "gtsplit returned: " << allele_vec[0];
// for( k=1; k<allele_vec.size(); k++){
// Rcpp::Rcout << "," << allele_vec[k];
// }
// Rcpp::Rcout << "\n";
// Initialize new vector of alleles with first element of allele_vec.
std::vector < std::string > allele_vec2;
// Scroll through vector looking for alleles.
for(k=0; k<allele_vec.size(); k++){
if( allele_vec[k] == "." ){
// Found missing value.
// Delete and bail out.
while( allele_vec2.size() > 0 ){
allele_vec2.erase( allele_vec2.begin() );
}
k = allele_vec.size();
} else if( allele_vec2.size() == 0 ){
// Initialize.
allele_vec2.push_back( allele_vec[k] );
} else if( allele_vec2[0] != allele_vec[k] ){
allele_vec2.push_back( allele_vec[k] );
}
}
// Rcpp::Rcout << "allele_vec2.size(): " << allele_vec2.size();
// Rcpp::Rcout << "\n";
// Rcpp::Rcout << "\n";
// Score return value.
if( allele_vec2.size() == 0){
if( na_is_false[0] == true ){
hets(i,j) = false;
} else if( na_is_false[0] == false ){
hets(i,j) = NA_LOGICAL;
}
} else if( allele_vec2.size() == 1){
hets(i,j) = false;
} else if( allele_vec2.size() > 1){
hets(i,j) = true;
}
}
}
return( hets );
}
