Skip to content

Commit

Permalink
replace std::cout with Rcpp::Rcout
Browse files Browse the repository at this point in the history
  • Loading branch information
@Zilong-Li
Zilong-Li committed Jul 16, 2024
1 parent f2f6581 commit 1e75274
Show file tree
Hide file tree
Showing 4 changed files with 57 additions and 50 deletions.
37 changes: 22 additions & 15 deletions STITCH/.Rbuildignore
View file
Original file line number Diff line number Diff line change
@@ -1,15 +1,22 @@
src/SeqLib/seq_test
src/SeqLib/.travis.scripts
src/SeqLib/fermi-lite/test
src/SeqLib/htslib/test
src/SeqLib/benchmark
src/SeqLib/Doxyfile
src/SeqLib/bwa/ChangeLog
src/SeqLib/bwa/bwakit/README.md
src/SeqLib/bwa/README.md
src/SeqLib/bwa/NEWS.md
src/SeqLib/bwa/README-alt.md
src/SeqLib/issue_tracking.md
src/SeqLib/README.md
src/SeqLib/fermi-lite/README.md
src/SeqLib/htslib/README.md
^LICENSE\.md$
^README\.Rmd$
^.*\.tbi$
^src/SeqLib/htslib/htscodecs/tests
^cran-comments\.md$
^CRAN-SUBMISSION$
\.git
\.github
\.cirrus.yml
\.appveyor.yml
\.clangd
\.clang-format
^Makefile
^README.html
.*\.tar\.gz$
.*\.tbi$
^.covrignore$
^codecov.yaml$
^\.github$
^_pkgdown\.yml$
^docs$
^pkgdown$
8 changes: 4 additions & 4 deletions STITCH/src/diploid.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,7 @@ arma::imat sample_diploid_path(const arma::mat & alphaHat_t, const arma::mat & t
for(kk = 0; kk < KK; kk++)
check = check + alphaHat_t(kk, T - 1);
if ((pow(check - 1, 2)) > 1e-4) {
std::cout << "BAD input assumption" << std::endl;
Rcpp::Rcout << "BAD input assumption" << std::endl;
return(sampled_path_diploid_t);
}
//
Expand Down Expand Up @@ -250,9 +250,9 @@ arma::imat sample_diploid_path(const arma::mat & alphaHat_t, const arma::mat & t
}
norm = alphaHat_t(prev_state, t + 1) / eMatGrid_t(prev_state, t + 1) / c(t + 1);
if ((pow(samp_vector_sum / norm - 1, 2)) > 1e-4) {
std::cout << "BAD COUNT on t=" << t << std::endl;
std::cout << "samp_vector_sum=" << samp_vector_sum << std::endl;
std::cout << "norm=" << norm << std::endl;
Rcpp::Rcout << "BAD COUNT on t=" << t << std::endl;
Rcpp::Rcout << "samp_vector_sum=" << samp_vector_sum << std::endl;
Rcpp::Rcout << "norm=" << norm << std::endl;
return(sampled_path_diploid_t);
}
// sample state using crazy C++
Expand Down
58 changes: 29 additions & 29 deletions STITCH/src/functions.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -133,9 +133,9 @@ double print_times(
) {
if( suppressOutput == 0 ) {
double cur=clock();
std::cout << std::setw (40) << past_text;
Rcpp::Rcout << std::setw (40) << past_text;
printf ("- %.6f cpu sec -", ((double)cur - (double)prev)* 1.0e-6);
std::cout << next_text << std::endl;
Rcpp::Rcout << next_text << std::endl;
prev=cur;
}
return prev;
Expand Down Expand Up @@ -197,7 +197,7 @@ Rcpp::LogicalVector rcpp_evaluate_bxtag(
int n_non_doub_zero;
int cur_qnameInteger = qnameInteger_ord(0);
for(int iCur = 0; iCur < n; iCur++) {
//std::cout << "iCur = " << iCur << " / " << n << std::endl;
//Rcpp::Rcout << "iCur = " << iCur << " / " << n << std::endl;
perform_check = false;
if (iCur == (n - 1)) {
perform_check = true;
Expand All @@ -206,17 +206,17 @@ Rcpp::LogicalVector rcpp_evaluate_bxtag(
perform_check = true;
}
}
//std::cout << "perform_check = " << perform_check << std::endl;
//Rcpp::Rcout << "perform_check = " << perform_check << std::endl;
if (perform_check) {
//std::cout << "------------------" << std::endl;
//Rcpp::Rcout << "------------------" << std::endl;
first_bxtag = "";
blank_local_bxtag = false;
n_non_doub_zero = 0;
for(int j = iStart; j <= iCur; j++) {
cur_bxtag = bxtag_ord(j);
//std::cout << "j = " << j << std::endl;
//std::cout << "first_bxtag = " << first_bxtag << std::endl;
//std::cout << "cur_bxtag = " << cur_bxtag << std::endl;
//Rcpp::Rcout << "j = " << j << std::endl;
//Rcpp::Rcout << "first_bxtag = " << first_bxtag << std::endl;
//Rcpp::Rcout << "cur_bxtag = " << cur_bxtag << std::endl;
if (cur_bxtag.find(doub_zero) == std::string::npos) {
// not found i.e. it has no double 00 so can use
n_non_doub_zero++;
Expand All @@ -228,7 +228,7 @@ Rcpp::LogicalVector rcpp_evaluate_bxtag(
}
}
}
//std::cout << "blank_local_bxtag = " << blank_local_bxtag << std::endl;
//Rcpp::Rcout << "blank_local_bxtag = " << blank_local_bxtag << std::endl;
}
// now afterwards, either blank out, or make the same
if (blank_local_bxtag) {
Expand All @@ -239,7 +239,7 @@ Rcpp::LogicalVector rcpp_evaluate_bxtag(
}
// also, if only one is zero
if ((n_non_doub_zero > 0) & ((iCur - iStart + 1) != n_non_doub_zero)) {
//std::cout << "apply rescue!" << std::endl;
//Rcpp::Rcout << "apply rescue!" << std::endl;
for(int j = iStart; j <= iCur; j++) {
bxtag_ord(j) = first_bxtag;
}
Expand Down Expand Up @@ -354,16 +354,16 @@ List cpp_read_reassign(
iReadStart = 0;
for (iRead = 0; iRead < nRawReads; iRead++ ) {
// if ((206 <= iRead) & (iRead <= 212)) {
// std::cout << "------------------------" << std::endl;
// std::cout << "iRead = " << iRead << std::endl;
// std::cout << "iReadStart = " << iReadStart << std::endl;
// std::cout << "curRead = " << curRead << std::endl;
// std::cout << "qnameInteger_ord[iRead + 1] = " << qnameInteger_ord[iRead + 1] << std::endl;
// Rcpp::Rcout << "------------------------" << std::endl;
// Rcpp::Rcout << "iRead = " << iRead << std::endl;
// Rcpp::Rcout << "iReadStart = " << iReadStart << std::endl;
// Rcpp::Rcout << "curRead = " << curRead << std::endl;
// Rcpp::Rcout << "qnameInteger_ord[iRead + 1] = " << qnameInteger_ord[iRead + 1] << std::endl;
// }
//
change_qname = qnameInteger_ord[iRead + 1] != curRead;
// if ((206 <= iRead) & (iRead <= 212)) {
// std::cout << "change_qname = " << change_qname << std::endl;
// Rcpp::Rcout << "change_qname = " << change_qname << std::endl;
// }
if (!use_bx_tag) {
save_condition_met = change_qname;
Expand All @@ -379,21 +379,21 @@ List cpp_read_reassign(
bx_tag_not_ok_to_continue = (change_bx_tag) | \
(bxtag_bad_ord[iRead]) | (bx_tag_distance_exceeded);
save_condition_met = change_qname & bx_tag_not_ok_to_continue;
//std::cout << " iRead = " << iRead << std::endl;
//std::cout << "bxtagInteger_ord[iRead + 1] = " << bxtagInteger_ord[iRead + 1] << std::endl;
//std::cout << " curbxtag = " << curbxtag << std::endl;
// std::cout << "change_bx_tag = " << change_bx_tag << std::endl;
// std::cout << "bxtag_bad_ord[iRead] = " << bxtag_bad_ord[iRead] << std::endl;
// std::cout << "bx_tag_distance_exceeded = " << bx_tag_distance_exceeded << std::endl;
//std::cout << " bx_tag_not_ok_to_continue = " << bx_tag_not_ok_to_continue << std::endl;
// std::cout << "change_qname = " << change_qname << std::endl;
//std::cout << " save_condition_met = " << save_condition_met << std::endl;
//Rcpp::Rcout << " iRead = " << iRead << std::endl;
//Rcpp::Rcout << "bxtagInteger_ord[iRead + 1] = " << bxtagInteger_ord[iRead + 1] << std::endl;
//Rcpp::Rcout << " curbxtag = " << curbxtag << std::endl;
// Rcpp::Rcout << "change_bx_tag = " << change_bx_tag << std::endl;
// Rcpp::Rcout << "bxtag_bad_ord[iRead] = " << bxtag_bad_ord[iRead] << std::endl;
// Rcpp::Rcout << "bx_tag_distance_exceeded = " << bx_tag_distance_exceeded << std::endl;
//Rcpp::Rcout << " bx_tag_not_ok_to_continue = " << bx_tag_not_ok_to_continue << std::endl;
// Rcpp::Rcout << "change_qname = " << change_qname << std::endl;
//Rcpp::Rcout << " save_condition_met = " << save_condition_met << std::endl;
}
if (change_qname) {
curRead = qnameInteger_ord[iRead + 1]; // + 1
}
if (save_condition_met) {
//std::cout << "SAVING WITH iReadStart = " << iReadStart << ", iRead = " << iRead << std::endl;
//Rcpp::Rcout << "SAVING WITH iReadStart = " << iReadStart << ", iRead = " << iRead << std::endl;
nSNPsInRead = -1; // this is 0-based (why did I do this)
minReadStart = 2147483647;
maxReadEnd = -1;
Expand All @@ -403,7 +403,7 @@ List cpp_read_reassign(
}
for(j = iReadStart; j <= iRead; j++) {
// check if we should be saving this bit
//std::cout << "j = " << j << ", save_this_read_check(j) = " << save_this_read_check(j) << std::endl;
//Rcpp::Rcout << "j = " << j << ", save_this_read_check(j) = " << save_this_read_check(j) << std::endl;
if (save_this_read_check(j)) {
r = ord[j];
if (use_bx_tag) {
Expand Down Expand Up @@ -465,8 +465,8 @@ List cpp_read_reassign(
sri_strand[count] = strand_to_out;
}
// if ((206 <= iRead) & (iRead <= 212)) {
// std::cout << " saving bit" << std::endl;
// std::cout << "count = " << count << std::endl;
// Rcpp::Rcout << " saving bit" << std::endl;
// Rcpp::Rcout << "count = " << count << std::endl;
// }
count++;
}
Expand Down
4 changes: 2 additions & 2 deletions STITCH/src/heuristics.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -84,11 +84,11 @@ Rcpp::NumericVector rcpp_make_smoothed_rate(
Rcpp::NumericVector smoothed_rate(nGrids - 1);
for(iGrid = 0; iGrid < (nGrids - 1); iGrid++) {
if (verbose) {
std::cout << "iGrid=" << iGrid << std::endl;
Rcpp::Rcout << "iGrid=" << iGrid << std::endl;
}
focal_point = (L_grid(iGrid) + L_grid(iGrid + 1)) / 2; // automatically rounded
if (verbose) {
std::cout << "focal_point=" << focal_point << std::endl;
Rcpp::Rcout << "focal_point=" << focal_point << std::endl;
}
//
// left
Expand Down

0 comments on commit 1e75274

Please sign in to comment.