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Added # as a character to be sanitized by VCFOutputRenderer. #5817

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merged 1 commit into from
Mar 19, 2019
Merged

Added # as a character to be sanitized by VCFOutputRenderer. #5817

merged 1 commit into from
Mar 19, 2019

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jonn-smith
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Also refactored the VcfOutputRenderer sanitization code.

Fixes #5671

@jonn-smith jonn-smith added this to the Engine-Q12019 milestone Mar 19, 2019
@jonn-smith jonn-smith requested a review from als364 March 19, 2019 19:40
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codecov-io commented Mar 19, 2019 •
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Codecov Report

Merging #5817 into master will increase coverage by 0.007%.
The diff coverage is 100%.

@@               Coverage Diff               @@
##              master     #5817       +/-   ##
===============================================
+ Coverage     87.029%   87.037%   +0.007%     
- Complexity     32104     32110        +6     
===============================================
  Files           1972      1972               
  Lines         147187    147194        +7     
  Branches       16201     16201               
===============================================
+ Hits          128096    128113       +17     
+ Misses         13184     13176        -8     
+ Partials        5907      5905        -2
Impacted Files Coverage Δ Complexity Δ
.../funcotator/FilterFuncotationsIntegrationTest.java 100% <ø> (ø) 5 <0> (ø) ⬇️
...e/hellbender/tools/funcotator/FuncotatorUtils.java 88.83% <100%> (+0.06%) 194 <1> (+1) ⬆️
...nder/tools/funcotator/FuncotatorUtilsUnitTest.java 92.6% <100%> (+0.024%) 88 <2> (+2) ⬆️
...nder/utils/runtime/StreamingProcessController.java 67.773% <0%> (+0.474%) 33% <0%> (ø) ⬇️
...nder/utils/io/DeleteRecursivelyOnExitPathHook.java 85% <0%> (+10%) 4% <0%> (+1%) ⬆️
...ithwaterman/SmithWatermanIntelAlignerUnitTest.java 90% <0%> (+30%) 2% <0%> (ø) ⬇️
...utils/smithwaterman/SmithWatermanIntelAligner.java 90% <0%> (+40%) 3% <0%> (+2%) ⬆️

@jonn-smith jonn-smith merged commit a9b62ce into master Mar 19, 2019
@jonn-smith jonn-smith deleted the jts_VCF_Output_Renderer_Hash_Clean_Fix_5671 branch March 19, 2019 21:32
@jonn-smith jonn-smith restored the jts_VCF_Output_Renderer_Hash_Clean_Fix_5671 branch March 19, 2019 21:35
@jonn-smith jonn-smith deleted the jts_VCF_Output_Renderer_Hash_Clean_Fix_5671 branch March 20, 2019 14:55
jonn-smith added a commit that referenced this pull request Mar 25, 2019
@jonn-smith
Added # as a character to be sanitized by VCFOutputRenderer. (#5817)
919ebf1 
Added in code to change how the best transcript is determined.
Changed how symbollic alleles are handled for GencodeFuncotation creation.

Fixes #5671
@jonn-smith jonn-smith mentioned this pull request Mar 25, 2019
Merged
jonn-smith added a commit that referenced this pull request Mar 26, 2019
@jonn-smith
Changed how symbollic alleles are handled for GencodeFuncotation crea…
6beef4f 
…tion. (#5834)

* Added `#` as a character to be sanitized by `VCFOutputRenderer`. (#5817)
* Added in code to change how the best transcript is determined.
* Changed how symbolic alleles are handled for `GencodeFuncotation` creation.

Fixes #5671
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@als364 als364 als364 approved these changes

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