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

feat(expected_coverage): use median coverage, fixes #1719 #1746

Merged
merged 2 commits into from
Dec 9, 2020
Merged

feat(expected_coverage): use median coverage, fixes #1719 #1746

merged 2 commits into from
Dec 9, 2020

Conversation

jemten
Copy link
Collaborator

@jemten jemten commented Dec 9, 2020

This PR adds | fixes:

  • see commit message

How to test:

  • Automatic and continuous test suite

Expected outcome:

  • Installation, unit and integration test suite pass

Review:

  • Code review
  • Tests pass

This version is a:

  • MAJOR - when you make incompatible API changes. If applicable record manual test results in PR header
  • MINOR - when you add functionality in a backwards compatible manner. If applicable record manual test results in PR header
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

@jemten jemten linked an issue Dec 9, 2020 that may be closed by this pull request
Consider changing from MEAN_TARGET_COVERAGE to MEDIAN_TARGET_COVERAGE for exome/panels #1719
Closed
henrikstranneheim
henrikstranneheim approved these changes Dec 9, 2020
View reviewed changes
Copy link
Collaborator

@henrikstranneheim henrikstranneheim left a comment

Choose a reason for hiding this comment

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

Great!

templates/grch38_mip_rd_dna_config.yaml
@@ -52,7 +52,6 @@ nist_call_set_vcf:
NA24143: grch38_nist_hg004_-na24143_v3.3.2-.vcf.gz
NA24385: grch38_nist_hg002_-na24385_v3.3.2-.vcf.gz
NA24631: grch38_nist_hg005_-na24631_v3.3.2-.vcf.gz
Copy link
Collaborator

Choose a reason for hiding this comment

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

Should we not use version 1.3 of qccollect_eval_metric_file here? Or is it a default?

Copy link
Collaborator Author

Choose a reason for hiding this comment

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

Yeah, it's default in the definition file. I see now that it is defined in all configs in the template and not only this one. I don't think we should have it in the config if the same file is already defined as default in the definition file. How do you feel about it?

Copy link
Collaborator

Choose a reason for hiding this comment

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

I agree! Let's remove it

@jemten jemten merged commit 7320210 into develop Dec 9, 2020
@jemten jemten deleted the feature/median_coverage branch December 9, 2020 15:36
@jemten jemten mentioned this pull request Mar 4, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@henrikstranneheim henrikstranneheim henrikstranneheim approved these changes

@ramprasadn ramprasadn Awaiting requested review from ramprasadn

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

Successfully merging this pull request may close these issues.

Consider changing from MEAN_TARGET_COVERAGE to MEDIAN_TARGET_COVERAGE for exome/panels
2 participants
@jemten @henrikstranneheim