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Use VariantEffect in TranscriptAnnotation #40

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ielis opened this issue Sep 14, 2023 · 0 comments · Fixed by #78
Closed

Use VariantEffect in TranscriptAnnotation #40

ielis opened this issue Sep 14, 2023 · 0 comments · Fixed by #78
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@ielis
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ielis commented Sep 14, 2023

Currently we represent variant effects as a strs in the TranscriptAnnotation. However, it would simplify the things down the line if we used VariantEffect enum members instead.

We need to require VariantEffects in TranscriptAnnotation and we should update all genophenocorr.preprocessing.FunctionalAnnotator implementations accordingly.

Definition of done

  • VariantEffect enum is moved to the genophenocorr.model package
  • use VariantEffect in TranscriptAnnotation
  • update the FunctionalAnnotator implementations
@lnrekerle lnrekerle self-assigned this Oct 10, 2023
@lnrekerle lnrekerle linked a pull request Oct 10, 2023 that will close this issue
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