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

Move GenomicsDB to 1.0.3 for Importer fix to Issue 5449 #5899

Merged
merged 1 commit into from
Apr 23, 2019

Conversation

nalinigans
Copy link
Collaborator

@nalinigans nalinigans commented Apr 22, 2019

@ldgauthier found a bug in GenomicsDBImport with overlapping deletions, specifically with the * allele and the deletion spanning the interval specified - see #5449 (comment). The fix for this issue(thanks @mlathara) is in 1.0.3 of GenomicsDB.

@codecov-io
Copy link

codecov-io commented Apr 22, 2019

Codecov Report

Merging #5899 into master will increase coverage by 0.001%.
The diff coverage is n/a.

@@               Coverage Diff               @@
##              master     #5899       +/-   ##
===============================================
+ Coverage     86.838%   86.838%   +0.001%     
- Complexity     32323     32324        +1     
===============================================
  Files           1991      1991               
  Lines         149327    149327               
  Branches       16483     16483               
===============================================
+ Hits          129672    129673        +1     
+ Misses         13647     13646        -1     
  Partials        6008      6008
Impacted Files Coverage Δ Complexity Δ
...lotypecaller/readthreading/ReadThreadingGraph.java 88.725% <0%> (-0.245%) 159% <0%> (ø)
...nder/utils/runtime/StreamingProcessController.java 68.72% <0%> (+0.948%) 34% <0%> (+1%) ⬆️

@nalinigans
Copy link
Collaborator Author

We have included unit tests for wildstar allele and the deletion spanning the interval in GenomicsDB. @ldgauthier, can you please confirm that this solves the issue?

Copy link
Contributor

@ldgauthier ldgauthier left a comment

Choose a reason for hiding this comment

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

I reran my exact use case and it works perfectly. Thanks for the quick turnaround!

@droazen droazen merged commit c644e20 into master Apr 23, 2019
@droazen droazen deleted the nalini_issue_5449 branch April 23, 2019 17:59
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.

4 participants