Completes #5260 on GitHub. #5464
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… by ';' in a VCF file.
…broke due to the change in the test file complexExample1.vcf. I modified the file testSelectVariants_KeepSelectionID.vcf appropriately so that the tests pass as they should.
davidbenjamin
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Nov 29, 2018
src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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MartonKN
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Nov 30, 2018
src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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src/main/java/org/broadinstitute/hellbender/engine/filters/VariantIDsVariantFilter.java
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.../java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java
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davidbenjamin
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davidbenjamin
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Nov 30, 2018
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@MartonKN Looks good! You can merge once tests pass. |
Codecov Report
@@ Coverage Diff @@
## master #5464 +/- ##
===============================================
- Coverage 86.986% 86.984% -0.002%
+ Complexity 31203 31201 -2
===============================================
Files 1909 1909
Lines 144195 144195
Branches 15951 15951
===============================================
- Hits 125429 125426 -3
- Misses 12997 13000 +3
Partials 5769 5769
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@MartonKN Don't forget to delete the branch. Note that a link to do so pops up when you merge a PR. |
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Changed SelectVariants so that it can handle multiple rsIDs separated by ';' in a VCF file.
The corresponding entry gets removed if any of those rsIDs has been set by the user to be deleted.
I also changed testExcludeSelectionIDFromFile() in SelectVariantsIntegrationTest to check this case.