SEXP appendListElements(SEXP r_list,
const std::vector<SEXP> &new_elements,
const std::vector<std::string> &new_element_names) {
if (new_element_names.size() != new_elements.size()) {
report_error("In appendListElements: The vector of new elements must "
"be the same size as the vector of new element names.");
}
int original_list_length = Rf_length(r_list);
SEXP ans;
PROTECT(ans = Rf_allocVector(
VECSXP, original_list_length + new_elements.size()));
for (int i = 0; i < original_list_length; ++i) {
SET_VECTOR_ELT(ans, i, VECTOR_ELT(r_list, i));
}
for (int i = 0; i < new_elements.size(); ++i) {
SET_VECTOR_ELT(ans, i + original_list_length,
new_elements[i]);
}
std::vector<std::string> new_list_names = getListNames(r_list);
for (int i = 0; i < new_element_names.size(); ++i) {
new_list_names.push_back(new_element_names[i]);
}
ans = setListNames(ans, new_list_names);
UNPROTECT(1);
return ans;
}
/**
* @param arg_fileName: a string character
* @param arg_geneFile: which gene file to use
* @param arg_geneName: which gene we are interested. (just allow One gene
* name).
*/
SEXP impl_readBGENToMatrixByGene(SEXP arg_fileName, SEXP arg_geneFile,
SEXP arg_geneName) {
SEXP ans = R_NilValue;
std::string FLAG_fileName = CHAR(STRING_ELT(arg_fileName, 0));
std::string FLAG_geneFile = CHAR(STRING_ELT(arg_geneFile, 0));
std::vector<std::string> FLAG_geneName;
extractStringArray(arg_geneName, &FLAG_geneName);
if (FLAG_fileName.size() == 0) {
error("Please provide BGEN file name");
}
if (FLAG_geneName.size() && FLAG_geneFile.size() == 0) {
error("Please provide gene file name when extract genotype by gene");
}
int nGene = FLAG_geneName.size();
Rprintf("%d region to be extracted.\n", nGene);
int numAllocated = 0;
// allocate return value
PROTECT(ans = allocVector(VECSXP, nGene));
numAllocated++;
setListNames(FLAG_geneName, &ans);
OrderedMap<std::string, std::string> geneRange;
loadGeneFile(FLAG_geneFile, FLAG_geneName, &geneRange);
for (int i = 0; i < nGene; ++i) {
// REprintf("range = %s\n", FLAG_geneName[i].c_str());
const std::string& range = geneRange[FLAG_geneName[i]];
// Rprintf( "range = %s\n", range.c_str());
BGenFile bin(FLAG_fileName);
if (range.size())
bin.setRangeList(range.c_str());
else {
warning("Gene name [ %s ] does not exists in provided gene file",
FLAG_geneName[i].c_str());
UNPROTECT(numAllocated);
return (ans);
};
// real working part
SET_VECTOR_ELT(ans, i, readBGEN2Matrix(&bin));
}
UNPROTECT(numAllocated);
return ans;
}
/**
* @param arg_fileName: a string character
* @param arg_geneFile: which gene file to use
* @param arg_geneName: which gene we are interested. (just allow One gene
* name).
*/
SEXP impl_readBGENToMatrixByRange(SEXP arg_fileName, SEXP arg_range) {
SEXP ans = R_NilValue;
std::string FLAG_fileName = CHAR(STRING_ELT(arg_fileName, 0));
std::vector<std::string> FLAG_range;
extractStringArray(arg_range, &FLAG_range);
if (FLAG_fileName.size() == 0) {
error("Please provide BGEN file name");
return ans;
}
if (FLAG_range.empty()) {
error("Please provide a given range, e.g. '1:100-200'");
return ans;
}
int nGene = FLAG_range.size();
Rprintf("%d region to be extracted.\n", nGene);
int numAllocated = 0;
// allocate return value
PROTECT(ans = allocVector(VECSXP, nGene));
numAllocated++;
setListNames(FLAG_range, &ans);
for (int i = 0; i < nGene; ++i) {
// REprintf("range = %s\n", FLAG_range[i].c_str());
BGenFile bin(FLAG_fileName);
bin.setRangeList(FLAG_range[i].c_str());
// real working part
SET_VECTOR_ELT(ans, i, readBGEN2Matrix(&bin));
}
UNPROTECT(numAllocated);
return ans;
} // end impl_readBGENToMatrixByRange
