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Funcotator: get the NCBI build version from the datasource config file #5522

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merged 1 commit into from
Jan 29, 2019

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droazen
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@droazen droazen commented Dec 13, 2018

Store the NCBI build version in the Gencode datasource config files
in order to resolve an issue where this value was not always available
when annotating IGR variants.

Resolves #4404

Store the NCBI build version in the Gencode datasource config files
in order to resolve an issue where this value was not always available
when annotating IGR variants.

Resolves #4404
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droazen commented Dec 13, 2018

Note that before this is merged, we'll need to do a datasource release in which the following property is added to the gencode config files:

# Required field for GENCODE files.
# NCBI build version:
ncbi_build_version = X

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Codecov Report

Merging #5522 into master will increase coverage by 0.002%.
The diff coverage is 100%.

@@              Coverage Diff               @@
##             master     #5522       +/-   ##
==============================================
+ Coverage     87.07%   87.073%   +0.002%     
  Complexity    31318     31318               
==============================================
  Files          1921      1921               
  Lines        144566    144563        -3     
  Branches      15950     15944        -6     
==============================================
+ Hits         125874    125875        +1     
  Misses        12900     12900               
+ Partials       5792      5788        -4
Impacted Files Coverage Δ Complexity Δ
...er/tools/funcotator/FuncotatorIntegrationTest.java 84.567% <ø> (+0.266%) 111 <0> (ø) ⬇️
...ools/funcotator/FuncotatorArgumentDefinitions.java 86.667% <100%> (+0.303%) 1 <0> (ø) ⬇️
...dataSources/gencode/GencodeFuncotationFactory.java 86.903% <100%> (+0.302%) 231 <5> (ø) ⬇️
...ender/tools/funcotator/FuncotationMapUnitTest.java 94.678% <100%> (ø) 38 <0> (ø) ⬇️
.../tools/funcotator/dataSources/DataSourceUtils.java 64.483% <100%> (+0.123%) 47 <0> (ø) ⬇️
...ces/gencode/GencodeFuncotationFactoryUnitTest.java 94.038% <100%> (+0.005%) 67 <1> (ø) ⬇️
...oadinstitute/hellbender/utils/gcs/BucketUtils.java 79.878% <0%> (-0.61%) 42% <0%> (ø)

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@jonn-smith jonn-smith left a comment

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This looks reasonable to me.

I have updated the data sources to include the field name, so it should be all up-to-date and working once merged.

@jonn-smith jonn-smith merged commit 11c7287 into master Jan 29, 2019
@jonn-smith jonn-smith deleted the dr_funcotator_query_ncbi_build_name branch January 29, 2019 14:06
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Funcotator - ncbiBuildName is not properly annotated for IGRs
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