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.

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: invalid paf produced for some patch alignments #274

Merged
merged 2 commits into from
Sep 24, 2024

Conversation

kdm9
Copy link
Contributor

@kdm9 kdm9 commented Sep 24, 2024

Fixes #273 (hopefully)

I will test this on my use case in the coming day, as it takes a while to run.

best,
K

@kdm9
Copy link
Contributor Author

kdm9 commented Sep 24, 2024

Alas this does not fix the issue, however there is something strange going on here. perhaps the conditional in question is not aln.ok but gap_compressed_identity >= min_identity

@kdm9
Copy link
Contributor Author

kdm9 commented Sep 24, 2024

regardless, those iv:Z and pt:Z tags are being printed for weird alignments that don't have the rest of the paf printed, breaking the PAF format & therefore seqwish.

@kdm9 kdm9 mentioned this pull request Sep 24, 2024
@kdm9
Copy link
Contributor Author

kdm9 commented Sep 24, 2024

Confirming that the latest commit fixes the issue for me.

@ekg
Copy link
Collaborator

ekg commented Sep 24, 2024

It looks right to me. Checking if the automated tests pass.

@ekg ekg merged commit 73c1331 into waveygang:main Sep 24, 2024
1 check passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Invalid PAF files produced
2 participants