Skip to content

Compute single-end MAPQ score better by considering at least two mappings. #600

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

Open
ksahlin wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Compute single-end MAPQ score better by considering at least two mappings. #600

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
6 changes: 4 additions & 2 deletions src/mapper.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -393,8 +393,10 @@ pub fn align_single_end_read(
// Use score-based dropoff: NAMs are sorted by score.
let score_dropoff = nam.score / nam_max.score;

if (tries > 1 && best_edit_distance == 0)
|| score_dropoff < mapping_parameters.dropoff_threshold
// Always extend at least the top-2 NAMs so that second_best_score is
// meaningful when computing MAPQ score.
if tries > 1
&& (best_edit_distance == 0 || score_dropoff < mapping_parameters.dropoff_threshold)
{
break;
}
Expand Down
Loading