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

Better error handling #9

Closed
4 tasks done
bepoli opened this issue Feb 15, 2023 · 0 comments · Fixed by #10
Closed
4 tasks done

Better error handling #9

bepoli opened this issue Feb 15, 2023 · 0 comments · Fixed by #10
Assignees
@bepoli
Labels
enhancement New feature or request
Milestone
v1.0.3

Comments

@bepoli
Copy link
Member

bepoli commented Feb 15, 2023 •
edited
Loading

The program should raise errors in case something in the input files is wrong, avoiding crashing with uninformative messages such as those dealt with in #1.
Keeping here a list of errors/exceptions to implement:

  • requirement not met (error if not present, warning if version is not supported)
  • cell barcode and UMI tags not found in BAM
  • BAM reference names not matching with BED
  • couldn't download the annotation data for a genome assembly (for any reason)
@bepoli bepoli added the enhancement New feature or request label Feb 15, 2023
@bepoli bepoli self-assigned this Feb 15, 2023
bepoli added a commit that referenced this issue Feb 17, 2023
@bepoli
handle requirement not met (#9)
ae209c8
@bepoli bepoli added this to the v1.0.3 milestone Feb 17, 2023
bepoli added a commit that referenced this issue Feb 17, 2023
@bepoli
add function to check for requirements (#9)
90468f3
bepoli added a commit that referenced this issue Feb 17, 2023
@bepoli
handle inconsistent chr names between BAM and BED (#9)
da3ad61
@bepoli bepoli linked a pull request Feb 17, 2023 that will close this issue
Better error handling #10
Merged
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@bepoli bepoli

Labels
enhancement New feature or request
Projects
None yet
Milestone
v1.0.3
Development

Successfully merging a pull request may close this issue.

Better error handling bodegalab/irescue
1 participant
@bepoli