Now can match between hg19 and b37 data sources. #5491
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- Fixed a NPE in the `problem` variant case, which is now resolved. This was due to not filling out the dataSourceName field. - Tested with b37 gnomAD matching against b37 variants with hg19 data sources. - Fixed some issues with the default problem variant annotations. - Adding in per-data source cache settings. - Fixing logger in DataSourceUtils. Fixes #5456
Codecov Report
@@ Coverage Diff @@
## master #5491 +/- ##
===============================================
- Coverage 87.069% 87.064% -0.004%
- Complexity 31244 31251 +7
===============================================
Files 1922 1922
Lines 144210 144253 +43
Branches 15916 15918 +2
===============================================
+ Hits 125562 125593 +31
- Misses 12874 12881 +7
- Partials 5774 5779 +5
|
LeeTL1220
approved these changes
Dec 7, 2018
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/DataSourceFuncotationFactory.java
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorArgumentCollection.java
Outdated
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/DataSourceUtils.java
Outdated
Show resolved
Hide resolved
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
Show resolved
Hide resolved
src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java
Outdated
Show resolved
Hide resolved
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
problemvariant case, which is now resolved.This was due to not filling out the dataSourceName field.
sources.
Fixes #5456