Rcpp::IntegerVector get_which(Rcpp::LogicalVector row) {
int j = 0;
for (int i = 0; i < row.length(); i++)
if (row(i))
j++;
Rcpp::IntegerVector ret(j);
for (int i = 0, j = 0; i < row.length(); i++)
if (row(i))
ret(j++) = i + 1; // R is 1-based
return ret;
}
// [[Rcpp::export]]
Rcpp::List subsetCounts(Rcpp::IntegerVector counts, Rcpp::IntegerVector start, Rcpp::IntegerVector width, Rcpp::LogicalVector strand){
if (start.length() != width.length() || start.length() != strand.length()) Rcpp::stop("provided vectors have different lengths...");
int nr = start.length();
int len = counts.length();
int tot = 0;
int* S = start.begin(); int* W = width.begin();
for (int i = 0; i < nr; ++i){
int s = S[i] - 1;
int w = W[i];
if (s < 0) Rcpp::stop("negative start positions are invalid");
if (s + w > len) Rcpp::stop("range exceeds the lengths of the counts vector");
tot += w;
}
Rcpp::IntegerVector res(tot);
Rcpp::IntegerVector nstart(nr);
Rcpp::IntegerVector nend(nr);
int* R = res.begin(); int* C = counts.begin(); int* ST = strand.begin();
int* NS = nstart.begin(); int* NE = nend.begin();
int currpos = 0;
for (int i = 0; i < nr; ++i){
NS[i] = currpos + 1;
int w = W[i];
if (ST[i]) std::copy(C + S[i]-1, C + S[i]-1 + w, R + currpos);
else std::reverse_copy(C + S[i]-1, C + S[i]-1 + w, R + currpos);
currpos += w;
NE[i] = currpos;
}
return List::create(_("counts")=res, _("starts")=nstart, _("ends")=nend);
}