Now non-locatable data sources can create funcotations again. #5774
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Primarily the large integration tests check for the non-locatable funcotation factories producing data. Regenerated the expected output from large tests. Fixes #5773
Codecov Report
@@ Coverage Diff @@
## master #5774 +/- ##
===============================================
+ Coverage 86.985% 86.998% +0.013%
- Complexity 31863 31871 +8
===============================================
Files 1943 1942 -1
Lines 146768 146789 +21
Branches 16223 16216 -7
===============================================
+ Hits 127666 127703 +37
+ Misses 13189 13177 -12
+ Partials 5913 5909 -4
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LeeTL1220
approved these changes
Mar 8, 2019
| @@ -292,7 +292,7 @@ if [[ $r -eq 0 ]] && ${doRunLargeTests} ; then | |||
| #INPUT=/Users/jonn/Development/gatk/src/test/resources/large/funcotator/regressionTestVariantSet2.vcf | |||
| #INPUT=/Users/jonn/Development/gatk/src/test/resources/large/funcotator/regressionTestHg19Large.vcf | |||
| #INPUT=/Users/jonn/Development/gatk/hg38_trio_liftoverb37.vcf | |||
| #INPUT=/Users/jonn/Development/gatk/tmp.vcf | |||
| INPUT=/Users/jonn/Development/gatk/tmp.vcf | |||
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Not sure why this is needed. What is this stuff?
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Left over from testing. I'll remove.
| @@ -135,6 +135,12 @@ public String getVersion() { | |||
| return version; | |||
| } | |||
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| /** | |||
| * @return {@code True} if this {@link DataSourceFuncotationFactory} requires features to create {@link Funcotation}s. {@code False} otherwise. | |||
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Any features? Or specific types? Please update docs.
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Yes - any features. If the DataSourceFuncotationFactory relies on feature matching that the GATK engine provides, then this should be true.
Things that don't require features (like gene name matching data sources) don't require any features to be present to create a funcotation.
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| final List<Funcotation> outputFuncotations; | ||
| // Only get features if we need them: |
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Can you collapse to one line? blah? truestuff: falsestuff
Added in another specific test for non-locatable data sources.
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Comments addressed. I also added in another test to check for this specific case and guard against it in the future. |
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Primarily the large integration tests check for the non-locatable
funcotation factories producing data.
Regenerated the expected output from large tests.
Fixes #5773