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

Rename test file so it doesn't masquerade as a Picard interval list. #5879

Merged
merged 1 commit into from
Apr 13, 2019

Conversation

cmnbroad
Copy link
Collaborator

When parsing interval arguments in GATK using the latest htsjdk, files that end in ".interval_list" are claimed by the new IntervalListCodec introduced in samtools/htsjdk#1327. This PR renames the one test file in GATK that has a Picard interval list file extension but isn't really a Picard interval list; without this change, CountReads and CountReadsSpark integration tests will fail when we upgrade to the next htsjdk.

@droazen droazen self-assigned this Apr 12, 2019
@droazen droazen self-requested a review April 12, 2019 15:12
Copy link
Contributor

@droazen droazen left a comment

Choose a reason for hiding this comment

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

👍 merge when ready @cmnbroad

@droazen droazen assigned cmnbroad and unassigned droazen Apr 12, 2019
@codecov-io
Copy link

codecov-io commented Apr 12, 2019

Codecov Report

Merging #5879 into master will not change coverage.
The diff coverage is 100%.

@@             Coverage Diff             @@
##              master     #5879   +/-   ##
===========================================
  Coverage     86.833%   86.833%           
- Complexity     32292     32293    +1     
===========================================
  Files           1990      1990           
  Lines         149107    149107           
  Branches       16477     16477           
===========================================
  Hits          129474    129474           
  Misses         13621     13621           
  Partials        6012      6012
Impacted Files Coverage Δ Complexity Δ
...te/hellbender/tools/CountReadsIntegrationTest.java 91.837% <100%> (ø) 11 <0> (ø) ⬇️
...park/pipelines/CountReadsSparkIntegrationTest.java 98.246% <100%> (ø) 9 <0> (ø) ⬇️
...lotypecaller/readthreading/ReadThreadingGraph.java 88.725% <0%> (-0.245%) 159% <0%> (ø)
...nder/utils/runtime/StreamingProcessController.java 67.773% <0%> (+0.474%) 33% <0%> (ø) ⬇️

@cmnbroad cmnbroad merged commit 7884afc into master Apr 13, 2019
@cmnbroad cmnbroad deleted the cn_bad_interval_list branch April 13, 2019 14:12
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.

3 participants