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

Jump to bottom

Force full-length ivar consensus builds #5115

Merged
merged 2 commits into from
Feb 10, 2023
Merged

Force full-length ivar consensus builds #5115

merged 2 commits into from
Feb 10, 2023

Conversation

wm75
Copy link
Contributor

@wm75 wm75 commented Feb 3, 2023

FOR CONTRIBUTOR:

  • - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • - License permits unrestricted use (educational + commercial)
  • - This PR adds a new tool or tool collection
  • - This PR updates an existing tool or tool collection
  • - This PR does something else (explain below)

@wm75
Force full-length ivar consensus builds
88c9ddc 
This requires the -a option of samtools mpileup or zero-coverage regions
at the ref sequence ends will silently be dropped and a truncated
consensus be produced.
@wm75
Copy link
Contributor Author

wm75 commented Feb 3, 2023

@pvanheus not quite sure how this one could go unnoticed until now.

@wm75 wm75 added the virology Issues related to better support for virology of SARS-CoV-2, MPXV and more. label Feb 3, 2023
@bernt-matthias
Copy link
Contributor

Please also check in the help section and report upstream https://github.com/andersen-lab/ivar/blob/d0e2ad0e6be69307771a5d36c573ffba578f4ce0/pipeline_consensus/Snakefile#L34

@wm75
More fixes to the consensus tool
40d1f00 
- Protect params against integer overflow
- Make "-n -" option work and simplify choice of min depth threshold action
@wm75
Copy link
Contributor Author

wm75 commented Feb 6, 2023

@bernt-matthias oh no, don't make me look into too much detail - only unearthing more bugs 🤯

@wm75
Copy link
Contributor Author

wm75 commented Feb 6, 2023

and report upstream

done in andersen-lab/ivar#144

@wm75
Copy link
Contributor Author

wm75 commented Feb 6, 2023

integer overflow issue reported, too: andersen-lab/ivar#145

@bernt-matthias
Copy link
Contributor

Then lets merge?

@wm75
Copy link
Contributor Author

wm75 commented Feb 10, 2023

Yes, I think so. Thanks for the review @bernt-matthias !

@wm75 wm75 merged commit fc9887d into galaxyproject:main Feb 10, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@bgruening bgruening bgruening approved these changes

Assignees
No one assigned
Labels
virology Issues related to better support for virology of SARS-CoV-2, MPXV and more.
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@wm75 @bernt-matthias @bgruening