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fix: gnomad_re should accept all nucleotide characters for ref/alt #276

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merged 3 commits into from
Nov 8, 2023
Merged

fix: gnomad_re should accept all nucleotide characters for ref/alt #276

merged 3 commits into from
Nov 8, 2023

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korikuzma
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Address #275 for main branch

@korikuzma korikuzma added bug Something isn't working priority:high High priority labels Nov 7, 2023
@korikuzma korikuzma self-assigned this Nov 7, 2023
@korikuzma korikuzma requested review from a team as code owners November 7, 2023 23:09
@korikuzma korikuzma mentioned this pull request Nov 7, 2023
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ahwagner
ahwagner approved these changes Nov 8, 2023
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VRS supports all IUPAC codes, this allows all IUPAC codes. Seems reasonable to me!

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We should remove . and * unless necessary for gnomAD expressions; in which case we need a method to handle them properly for VRS (these are not valid IUPAC nucleotide characters).

src/ga4gh/vrs/extras/translator.py Outdated Show resolved Hide resolved
korikuzma and others added 2 commits November 8, 2023 11:53
@korikuzma @ahwagner
Update src/ga4gh/vrs/extras/translator.py
6554829 
Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
@korikuzma
update tests with gnomad_re update
98eb9d9
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Confirmed with gnomAD team that ALT will never be ..

@korikuzma korikuzma merged commit 0419979 into main Nov 8, 2023
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@korikuzma korikuzma deleted the issue-275 branch November 8, 2023 21:00
korikuzma added a commit that referenced this pull request Nov 8, 2023
@korikuzma @ahwagner
fix: gnomad_re should accept all nucleotide characters for ref/alt (#276
a3f7ec6 
)

Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
korikuzma added a commit that referenced this pull request Nov 8, 2023
@korikuzma @ahwagner
fix: gnomad_re should accept all nucleotide characters for ref/alt (#276
46d0c98 
)

Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
korikuzma added a commit that referenced this pull request Nov 8, 2023
@korikuzma @ahwagner
fix: gnomad_re should accept all nucleotide characters for ref/alt (#276
152d243 
) (#277)

Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
korikuzma added a commit that referenced this pull request Nov 8, 2023
@korikuzma @ahwagner
fix: gnomad_re should accept all nucleotide characters for ref/alt (#276
39b24f7 
) (#278)

Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
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@toneillbroad toneillbroad toneillbroad approved these changes

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