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Funcotator fix for missing Match_Norm_Seq_Allele1 and Match_Norm_Seq_Allele2 #7422

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merged 4 commits into from
Aug 18, 2021
Merged

Funcotator fix for missing Match_Norm_Seq_Allele1 and Match_Norm_Seq_Allele2 #7422

merged 4 commits into from
Aug 18, 2021

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jonn-smith
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@jonn-smith jonn-smith commented Aug 17, 2021 •
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  • Added code to populate Match_Norm_Seq_Allele1 and 2.
  • Added two samples to regressionTestVariantSetHG38.vcf file.
  • Regenerated and validated expected outputs for large tests.

Fixes #7408

@jonn-smith
Added code to populate Match_Norm_Seq_Allele1 and 2.
5355aad 
Still needs tests.
Fixes #7408
@jonn-smith
Added tests for code changes.
82f9ae6 
- Added two samples to regressionTestVariantSetHG38.vcf file.
- Regenerated and validated expected outputs for large tests.
@jonn-smith jonn-smith requested a review from droazen August 17, 2021 22:39
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gatk-bot commented Aug 17, 2021 •
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Travis reported job failures from build 35555
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 35555.13 logs
unit openjdk8 35555.3 logs

@jonn-smith jonn-smith mentioned this pull request Aug 18, 2021
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droazen
droazen approved these changes Aug 18, 2021
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👍 @jonn-smith Merge once tests pass and you're satisfied with the test coverage for the fix

@droazen droazen assigned jonn-smith and unassigned droazen Aug 18, 2021
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gatk-bot commented Aug 18, 2021 •
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Travis reported job failures from build 35564
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 35564.13 logs
unit openjdk8 35564.3 logs

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droazen commented Aug 18, 2021

@jonn-smith Looks like there are 3 failures in CustomMafFuncotationCreatorUnitTest on the latest run

@droazen droazen merged commit f16cc95 into master Aug 18, 2021
@droazen droazen deleted the jts_match_norm_fix_7408 branch August 18, 2021 23:23
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@droazen droazen droazen approved these changes

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Funcotator not populating Match_Norm_Seq_Allele1 and Match_Norm_Seq_Allele2 when generating MAF
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