Addressing issue #4712 #4770
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Addressing issue #4712 #4770
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Added in a script to pull down the latest Gencode data source. Fixed an issue in 5' UTR processing that would cause variant alleles with length > 1 to throw an exception (issue 4712). Added three test cases to prevent regression of issue 4712. Updated Gencode codec to be compatible with latest Gencode release (v28). Fixed a bug in the version detection for Funcotator data sources that would prevent newer data source versions from being detected as compatible (date comparison error).
Codecov Report
@@ Coverage Diff @@
## master #4770 +/- ##
===============================================
- Coverage 80.097% 80.095% -0.002%
- Complexity 17402 17406 +4
===============================================
Files 1080 1080
Lines 63067 63076 +9
Branches 10174 10181 +7
===============================================
+ Hits 50515 50521 +6
- Misses 8566 8569 +3
Partials 3986 3986
|
LeeTL1220
reviewed
May 15, 2018
| @@ -181,20 +181,26 @@ private static void addManualAnnotationsToArguments(final ArgumentsBuilder argum | |||
| @DataProvider | |||
| public Object[][] provideForLargeDataValidationTest() { | |||
| return new Object[][] { | |||
| // { | |||
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Can we get rid of commented code?
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Comments were added for testing, but these are valid tests that should be preserved.
Comments removed!
| @@ -1074,32 +1073,38 @@ private GencodeFuncotation createUtrFuncotation(final VariantContext variant, | |||
| // Get the 5' UTR sequence here. | |||
| // Note: We grab 3 extra bases at the end (from the coding sequence) so that we can check for denovo starts | |||
| // even if the variant occurs in the last base of the UTR. | |||
| final int numExtraLeadingBases = 2; | |||
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Added in a script to pull down the latest Gencode data source.
Fixed an issue in 5' UTR processing that would cause variant alleles with length > 1 to throw an exception (issue 4712).
Added three test cases to prevent regression of issue 4712.
Updated Gencode codec to be compatible with latest Gencode release (v28).
Fixed a bug in the version detection for Funcotator data sources that would prevent newer data source versions from being detected as compatible (date comparison error).