Skip to content

surject: rank paths by their best alignment #5009

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

Draft
Sagorikanag wants to merge 1 commit into
base: master
Choose a base branch
from
+17 −18
Draft

surject: rank paths by their best alignment #5009

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
35 changes: 17 additions & 18 deletions src/surjector.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -493,37 +493,36 @@ using namespace std;
if (multimap_to_all_paths) {
vector<tuple<int32_t, path_handle_t, bool>> path_strands;
if (source_aln) {
// give each path strand the alignment score if it is primary or 0 if it is supplementary (to deprioritize)
// Rank each path strand by its best non-supplementary surjection.
for (const auto& strand_surjections : aln_surjections) {
bool all_supplementary = false;
bool found_non_supplementary = false;
int32_t best_score = numeric_limits<int32_t>::min();
for (const auto& surjection : strand_surjections.second) {
if (!is_supplementary(surjection.first)) {
all_supplementary = false;
path_strands.emplace_back(surjection.first.score(),
strand_surjections.first.first, strand_surjections.first.second);
break;
found_non_supplementary = true;
best_score = max(best_score, surjection.first.score());
}
}
if (all_supplementary) {
path_strands.emplace_back(0, strand_surjections.first.first, strand_surjections.first.second);
}
path_strands.emplace_back(found_non_supplementary ? best_score : 0,
strand_surjections.first.first,
strand_surjections.first.second);
}
}
else {
// give each path strand the primary alignment score if it is primary or 0 if it is supplementary (to deprioritize)
// Rank each path strand by its best non-supplementary surjection.
for (const auto& strand_surjections : mp_aln_surjections) {
bool all_supplementary = false;
bool found_non_supplementary = false;
int32_t best_score = numeric_limits<int32_t>::min();
for (const auto& surjection : strand_surjections.second) {
if (!is_supplementary(surjection.first)) {
all_supplementary = false;
path_strands.emplace_back(optimal_alignment_score(surjection.first, allow_negative_scores),
strand_surjections.first.first, strand_surjections.first.second);
break;
found_non_supplementary = true;
best_score = max(best_score, optimal_alignment_score(surjection.first,
allow_negative_scores));
}
}
if (all_supplementary) {
path_strands.emplace_back(0, strand_surjections.first.first, strand_surjections.first.second);
};
path_strands.emplace_back(found_non_supplementary ? best_score : 0,
strand_surjections.first.first,
strand_surjections.first.second);
}
}
sort(path_strands.begin(), path_strands.end(), greater<decltype(path_strands)::value_type>());
Expand Down
Loading