Skip to content

Half-mapped pairs go through the same selection and filters as pairs #367

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
BenjaminDEMAILLE wants to merge 1 commit into
base: perf/hotpaths
Choose a base branch
from
Open

Half-mapped pairs go through the same selection and filters as pairs #367

Show file tree
Hide file tree
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: 6 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@ Sections commonly used: Features, Bug fixes, Other changes.

### Bug fixes

- A pair with one aligned mate is no longer reported as one unique location. Single-mate
alignments now compete with pairs for the score range, the primary and `NH`, and pass the
same `mappedFilter` and `--outFilterMultimapNmax` checks: a mate in a 3-copy repeat gets
`NH:3 MAPQ:1` on all 3 copies. The unmapped mate's record is written only under
`--outSAMunmapped Within`, after the read's alignments; `Within KeepPairs` writes one after
each single-mate alignment. `NH` of a pair also counts alignments past `--outSAMmultNmax`.
- The residual differences in DIVERGENCE.md §5 are fixed. On the parity
suite's yeast (10k and 100k, SE and PE, chimeric, `--outSAMunmapped
Within`), human chr21 (SE, PE) and fusion runs, alignments, `SJ.out.tab`
Expand Down
388 changes: 177 additions & 211 deletions src/align/read_align.rs
View file
Open in desktop

Large diffs are not rendered by default.

Loading
Loading