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

Fixes for -min and -max parameters #234

Merged
merged 4 commits into from
Oct 9, 2024
Merged

Fixes for -min and -max parameters #234

merged 4 commits into from
Oct 9, 2024

Conversation

lcoombe
Copy link
Member

@lcoombe lcoombe commented Oct 9, 2024

  • Genome and metagenome modes: Add extra check before writing read to file to avoid reads that are slightly out of the specified length range
    • Same for unaligned reads
  • Clarified in the transcriptome help page that -min and -max are only used for unaligned reads (min_len and max_len options. #160)
  • To be consistent with genome mode, don't allow --perfect and --chimeric reads simultaneously in metagenome mode

lcoombe added 4 commits October 9, 2024 12:19
@lcoombe
Add extra length check for genome mode
5307b56
@lcoombe
Extra check for lengths when simulating unaligned reads, update READM…
8c0bdf3 
…E.md

- Clarify that the -min and -max parameters in transcriptome mode are ONLY used for unaligned read simulation
@lcoombe
Add extra checks for min/max lengths in metagenome mode
06415dc
@lcoombe
Don't allow --chimeric and --perfect in metagenome mode
59dfc2d 
- counter-intuitive to have chimeric reads in perfect mode
- This update is consistent with genome mode
@lcoombe lcoombe requested a review from parham-k October 9, 2024 19:21
parham-k
parham-k approved these changes Oct 9, 2024
View reviewed changes
Copy link
Member

@parham-k parham-k left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good. Thanks @lcoombe.

@lcoombe lcoombe merged commit 54a49aa into master Oct 9, 2024
@lcoombe lcoombe deleted the fix_min_max branch October 9, 2024 21:13
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@parham-k parham-k parham-k approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@lcoombe @parham-k