// [[Rcpp::export]]
void write_vcf_body( Rcpp::CharacterMatrix fix,
Rcpp::CharacterMatrix gt,
std::string filename,
int mask=0 ) {
// http://stackoverflow.com/a/5649224
//
int verbose = 0;
// int verbose = 1;
if( verbose == 1 ){
Rcpp::Rcout << "Made it into the function!\n";
}
int i = 0; // Rows
int j = 0; // Columns
std::string tmpstring; // Assemble each line before writing
// Initialize filehandle.
gzFile fi;
// Initialize file.
// Note that gzfile does not tolerate initializing an empty file.
// Use ofstream instead.
if ( ! std::ifstream( filename ) ){
if( verbose == 1 ){
Rcpp::Rcout << "File does not exist." << std::endl;
}
std::ofstream myfile;
myfile.open (filename, std::ios::out | std::ios::binary);
myfile.close();
// This should make valgrind hang.
// Or not???
// fi = gzopen( filename.c_str(), "ab" );
// gzclose(fi);
}
// In order for APPEND=TRUE to work the header
// should not be printed here.
if( verbose == 1 ){
Rcpp::Rcout << "Matrix fix has " << fix.nrow() << " rows (variants).\n";
}
// Manage body
if( fix.nrow() >= 1 ){
if( verbose == 1 ){
Rcpp::Rcout << "Processing the body (variants).\n";
}
// There is at least one variant.
fi = gzopen( filename.c_str(), "ab" );
if (! fi) {
Rcpp::Rcerr << "gzopen of " << filename << " failed: " << strerror (errno) << ".\n";
}
for(i = 0; i < fix.nrow(); i++){
Rcpp::checkUserInterrupt();
if(mask == 1 && fix(i,6) != "PASS" ){
// Don't print variant.
} else {
// Print variant.
j = 0;
tmpstring = fix(i,j);
for(j = 1; j < fix.ncol(); j++){
if(fix(i,j) == NA_STRING){
tmpstring = tmpstring + "\t" + ".";
} else {
tmpstring = tmpstring + "\t" + fix(i,j);
}
}
// gt portion
for(j = 0; j < gt.ncol(); j++){
if(gt(i, j) == NA_STRING){
tmpstring = tmpstring + "\t" + "./.";
} else {
tmpstring = tmpstring + "\t" + gt(i, j);
}
}
gzwrite(fi, tmpstring.c_str(), tmpstring.size());
gzwrite(fi,"\n",strlen("\n"));
}
}
if( verbose == 1 ){
Rcpp::Rcout << "Finished processing the body (variants).\n";
}
gzclose(fi);
} else {
if( verbose == 1 ){
Rcpp::Rcout << "No rows (variants).\n";
}
}
// return void;
}
// [[Rcpp::export]]
Rcpp::DataFrame gt_to_popsum(Rcpp::DataFrame var_info, Rcpp::CharacterMatrix gt) {
// Calculate popgen summaries for the sample.
// var_info should contain columns named 'CHROM', 'POS', 'mask' and possibly others.
Rcpp::LogicalVector mask = var_info["mask"];
Rcpp::IntegerVector nsample(mask.size());
Rcpp::StringVector allele_counts(mask.size());
Rcpp::NumericVector Hes(mask.size());
Rcpp::NumericVector Nes(mask.size());
int i = 0;
int j = 0;
int k = 0;
for(i=0; i < gt.nrow(); i++){ // Iterate over variants (rows)
if(mask[i] == TRUE){
std::vector<int> myalleles (1,0);
for(j=0; j < gt.ncol(); j++){ // Iterate over samples (columns)
if(gt(i, j) != NA_STRING){
nsample[i]++; // Increment sample count.
// Count alleles per sample.
std::vector < int > intv = gtsplit(as<std::string>(gt(i, j)));
for(k=0; k<intv.size(); k++){
while(myalleles.size() - 1 < intv[k]){
// We have more alleles than exist in the vector myalleles.
myalleles.push_back(0);
}
myalleles[intv[k]]++;
}
}
}
// Concatenate allele counts into a comma delimited string.
int n;
char buffer [50];
n = sprintf (buffer, "%d", myalleles[0]);
for(j=1; j < myalleles.size(); j++){
n=sprintf (buffer, "%s,%d", buffer, myalleles[j]);
}
allele_counts[i] = buffer;
// Sum all alleles.
int nalleles = myalleles[0];
for(j=1; j < myalleles.size(); j++){
nalleles = nalleles + myalleles[j];
}
// Stats.
double He = 1;
He = He - pow(double(myalleles[0])/double(nalleles), myalleles.size());
for(j=1; j < myalleles.size(); j++){
He = He - pow(double(myalleles[j])/double(nalleles), myalleles.size());
}
Hes[i] = He;
Nes[i] = 1/(1-He);
} else { // Missing variant (row=NA)
nsample[i] = NA_INTEGER;
}
}
return Rcpp::DataFrame::create(var_info,
_["n"]=nsample,
_["Allele_counts"]=allele_counts,
_["He"]=Hes,
_["Ne"]=Nes
);
}
//' @export
// [[Rcpp::export(name=".gt_to_popsum")]]
Rcpp::DataFrame gt_to_popsum(Rcpp::DataFrame var_info, Rcpp::CharacterMatrix gt) {
// Calculate popgen summaries for the sample.
// var_info should contain columns named 'CHROM', 'POS', 'mask' and possibly others.
Rcpp::LogicalVector mask = var_info["mask"];
Rcpp::IntegerVector nsample(mask.size());
Rcpp::StringVector allele_counts(mask.size());
Rcpp::NumericVector Hes(mask.size());
Rcpp::NumericVector Nes(mask.size());
int i = 0;
int j = 0;
// unsigned int j = 0;
unsigned int k = 0;
for(i=0; i < gt.nrow(); i++){ // Iterate over variants (rows)
if(mask[i] == TRUE){
std::vector<int> myalleles (1,0);
for(j=0; j < gt.ncol(); j++){ // Iterate over samples (columns)
if(gt(i, j) != NA_STRING){
nsample[i]++; // Increment sample count.
// Rcout << "gt: " << gt(i, j) << "\n";
// Count alleles per sample.
int unphased_as_na = 0; // 0 == FALSE
std::vector < std::string > gt_vector;
std::string gt2 = as<std::string>(gt(i,j));
vcfRCommon::gtsplit( gt2, gt_vector, unphased_as_na );
// Rcout << "gt_vector.size: " << gt_vector.size() << "\n";
for(k=0; k<gt_vector.size(); k++){
int myAllele = std::stoi(gt_vector[k]);
// Rcout << " " << myAllele;
// // If this genotype had an allele we did not previously observe
// we'll have to grow the vector.
while(myalleles.size() - 1 < myAllele){
myalleles.push_back(0);
}
myalleles[myAllele]++;
}
// Rcout << "\n\n";
}
}
// Concatenate allele counts into a comma delimited string.
char buffer [50];
// int n;
// n=sprintf(buffer, "%d", myalleles[0]);
sprintf(buffer, "%d", myalleles[0]);
for(j=1; (unsigned)j < myalleles.size(); j++){
// n=sprintf (buffer, "%s,%d", buffer, myalleles[j]);
sprintf (buffer, "%s,%d", buffer, myalleles[j]);
}
allele_counts[i] = buffer;
// Sum all alleles.
int nalleles = myalleles[0];
for(j=1; (unsigned)j < myalleles.size(); j++){
nalleles = nalleles + myalleles[j];
}
// Stats.
double He = 1;
He = He - pow(double(myalleles[0])/double(nalleles), myalleles.size());
for(j=1; (unsigned)j < myalleles.size(); j++){
He = He - pow(double(myalleles[j])/double(nalleles), myalleles.size());
}
Hes[i] = He;
Nes[i] = 1/(1-He);
} else { // Missing variant (row=NA)
nsample[i] = NA_INTEGER;
}
}
return Rcpp::DataFrame::create(var_info,
_["n"]=nsample,
_["Allele_counts"]=allele_counts,
_["He"]=Hes,
_["Ne"]=Nes
);
}