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update vcf2json (and other modules that translate Mongo to FHIR) #87

Merged
merged 6 commits into from
May 24, 2024
Merged

update vcf2json (and other modules that translate Mongo to FHIR) #87

merged 6 commits into from
May 24, 2024

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rhdolin
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@rhdolin rhdolin commented May 23, 2024

  • fix vcf2json phase data generation
  • fix vcf2json multi-allelic ALT translation
  • add 'Variants.allelicFrequency' in Mongo and remove Variants.ADS and Variants.DP
  • app/common.py - fix SV inner and outer start calculations
  • app/common.py - revise to use Variants.allelicFrequency
  • refresh all data (to have correct molecular consequence data)
  • update tests

@rhdolin
update vcf2json (and other modules that correspondingly translate Mon…
67a9e90 
…go output into FHIR)

- fix vcf2json phase data generation
- fix vcf2json multi-allelic ALT translation
- add 'Variants.allelicFrequency' in Mongo and remove Variants.ADS and Variants.DP
- app/common.py - fix SV inner and outer start calculations
- app/common.py - revise to use Variants.allelicFrequency
- refresh all data (to have correct molecular consequence data)
- update tests
@rhdolin rhdolin requested a review from mihaitodor May 23, 2024 21:42
mihaitodor
mihaitodor approved these changes May 24, 2024
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Looks good to me, just noticed a minor nit. Feel free to :shipit:

utilities/vcf2json.py Outdated Show resolved Hide resolved
@rhdolin rhdolin merged commit c4208e6 into main May 24, 2024
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@mihaitodor mihaitodor mihaitodor approved these changes

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@rhdolin @mihaitodor