Force full-length ivar consensus builds#5115
Merged
wm75 merged 2 commits intogalaxyproject:mainfrom Feb 10, 2023
Merged
Conversation
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.
Member
Author
|
@pvanheus not quite sure how this one could go unnoticed until now. |
wm75
added
the
virology
bgruening
approved these changes
Feb 3, 2023
Contributor
|
Please also check in the help section and report upstream https://github.com/andersen-lab/ivar/blob/d0e2ad0e6be69307771a5d36c573ffba578f4ce0/pipeline_consensus/Snakefile#L34 |
- Protect params against integer overflow - Make "-n -" option work and simplify choice of min depth threshold action
Member
Author
|
@bernt-matthias oh no, don't make me look into too much detail - only unearthing more bugs 🤯 |
Member
Author
done in andersen-lab/ivar#144 |
Member
Author
|
integer overflow issue reported, too: andersen-lab/ivar#145 |
Contributor
|
Then lets merge? |
Member
Author
|
Yes, I think so. Thanks for the review @bernt-matthias ! |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
FOR CONTRIBUTOR: