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

better error message for crosscheck when dictionary checks fail. #1982

Merged
merged 1 commit into from
Dec 10, 2024

Conversation

yfarjoun
Copy link
Contributor

@yfarjoun yfarjoun commented Nov 26, 2024

Description

when many files are included in a crosscheck and a few of the files contain a problematic dictionary the exception will appear after all the files have been processed, but the error message will not inform the user of the problematic file(s). This change solves that by wrapping the fingerprinting calls in a try/catch and logging an error when this happens.

Moves the log message above the checkdictionary call and wraps fingerprinting in a try/catch to get an informative error message regarding the name of the file that caused the problem


Checklist (never delete this)

Never delete this, it is our record that procedure was followed. If you find that for whatever reason one of the checklist points doesn't apply to your PR, you can leave it unchecked but please add an explanation below.

Content

  • Added or modified tests to cover changes and any new functionality
  • Edited the README / documentation (if applicable)
  • All tests passing on github actions

Review

  • Final thumbs-up from reviewer
  • Rebase, squash and reword as applicable

For more detailed guidelines, see https://github.com/broadinstitute/picard/wiki/Guidelines-for-pull-requests

@yfarjoun yfarjoun changed the title better error message better error message for crosscheck when dictionary checks fail. Nov 26, 2024
Copy link
Member

@lbergelson lbergelson left a comment

Choose a reason for hiding this comment

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

@yfarjoun Thanks! Sorry I didn't notice this sooner.

@lbergelson lbergelson merged commit 306401a into broadinstitute:master Dec 10, 2024
6 checks 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.

2 participants