Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix position to print all paths for all bed regions #453

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Fix position to print all paths for all bed regions #453

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
bf891f3
enable position to print all paths for all bed regions
ASLeonard Oct 10, 2022
6b8665b
Merge branch 'pangenome:master' into master
ASLeonard Dec 1, 2022
876e777
Merge branch 'pangenome:master' into master
ASLeonard Apr 11, 2023
8aba4dc
Merge branch 'pangenome:master' into master
ASLeonard Apr 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 24 additions & 17 deletions src/subcommand/position_main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -619,7 +619,8 @@ int main_position(int argc, char** argv) {
const hash_set<uint64_t>& path_set,
const pos_t& pos, lift_result_t& lift,
const step_handle_t target_step_handle,
const bool path_jaccard) {
const bool path_jaccard,
const path_handle_t* target_path=NULL) {
// unpacking our args
int64_t& path_offset = lift.path_offset;
step_handle_t& ref_hit = lift.ref_hit;
Expand All @@ -646,7 +647,7 @@ int main_position(int argc, char** argv) {
graph.for_each_step_on_handle(
h, [&](const step_handle_t& s) {
auto p = graph.get_path_handle_of_step(s);
if (!got_hit && path_set.count(as_integer(p))) {
if (!got_hit && path_set.count(as_integer(p)) && (target_path==NULL||p==*target_path)) {
//std::cerr << "thought I got a hit" << std::endl;
got_hit = true;
hit = s;
Expand Down Expand Up @@ -894,22 +895,28 @@ int main_position(int argc, char** argv) {
std::cout << path_range.data << "\t"
<< id(pos_begin) << "," << offset(pos_begin) << "," << (is_rev(pos_begin)?"-":"+") << "\t"
<< id(pos_end) << "," << offset(pos_end) << "," << (is_rev(pos_end)?"-":"+") << std::endl;
} else if (get_position(target_graph, ref_path_set, pos_begin, lift_begin, step_handle_graph_pos_begin, true)
&& get_position(target_graph, ref_path_set, pos_end, lift_end, step_handle_graph_pos_end, true)) {
bool ref_is_rev = false;
path_handle_t p_begin = target_graph.get_path_handle_of_step(lift_begin.ref_hit);
path_handle_t p_end = target_graph.get_path_handle_of_step(lift_end.ref_hit);
// XXX TODO assert these to be equal......
} else {

for (const path_handle_t& P: ref_paths) {
if (get_position(target_graph, ref_path_set, pos_begin, lift_begin, step_handle_graph_pos_begin, true,&P)
&& get_position(target_graph, ref_path_set, pos_end, lift_end, step_handle_graph_pos_end, true,&P)) {

bool ref_is_rev = false;
path_handle_t p_begin = target_graph.get_path_handle_of_step(lift_begin.ref_hit);
path_handle_t p_end = target_graph.get_path_handle_of_step(lift_end.ref_hit);
// XXX TODO assert these to be equal......
#pragma omp critical (cout)
std::cout << path_range.data << "\t"
<< target_graph.get_path_name(p_begin) << ","
<< lift_begin.path_offset << ","
<< (lift_begin.is_rev_vs_ref ? "-" : "+") << "\t"
<< target_graph.get_path_name(p_end) << ","
<< lift_end.path_offset << ","
<< (lift_end.is_rev_vs_ref ? "-" : "+") << "\t"
<< (lift_begin.is_rev_vs_ref ^ path_range.is_rev ? "-" : "+") << std::endl;
//<< walked_to_hit_ref << "\t" << (is_rev_vs_ref ? "-" : "+") << std::endl;
std::cout << path_range.data << "\t"
<< target_graph.get_path_name(p_begin) << ","
<< lift_begin.path_offset << ","
<< (lift_begin.is_rev_vs_ref ? "-" : "+") << "\t"
<< target_graph.get_path_name(p_end) << ","
<< lift_end.path_offset << ","
<< (lift_end.is_rev_vs_ref ? "-" : "+") << "\t"
<< (lift_begin.is_rev_vs_ref ^ path_range.is_rev ? "-" : "+") << std::endl;
//<< walked_to_hit_ref << "\t" << (is_rev_vs_ref ? "-" : "+") << std::endl;
}
}
}
}
}
Expand Down