Code

Refactor vrs_map to use mavehgvs#1

Code

Merged

sallybg merged 16 commits intodevVariantEffect/dcd_mapping2:devfrom bencap/upstream-integrationVariantEffect/dcd_mapping2:bencap/upstream-integrationCopy head branch name to clipboardJun 14, 2024

+4,078-236

Commits

Commits on Jun 3, 2024

• Initialize Docker dev environment and require Python 3.11

  

  sallybg

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• First working version of Sally's notebook with VRS 2.0

  

  sallybg

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• Getting this working in docker. Note that

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  nickzoic

  authored and

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• neaten up deps for gene_normalizer

  

  nickzoic

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• Download Reference Sequence as part of Docker Build Step

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• Variable type clarification

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Commits on Jun 14, 2024

• Add mavehgvs parsing for single-position variants

  sallybg

  committed
  84f05b4

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• Add Samtools to Dockerfile

  

  bencap

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  1d7ce30

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• Only run checks on 3.11+

  

  bencap

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  fe093c2

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• Don't close db conn during seqrepo check

  sallybg

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  5a3674b

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• Refactor vrs_map to use mavehgvs

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  09f5088

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• Remove tests for variants with '?' character in hgvs string

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  sallybg

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• nb: add experiment data

  

  jsstevenson

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  committed
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• nb: update figure params

  

  jsstevenson

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• Handle NoneType variant sequences

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  sallybg

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• Output all mappings unless preferred layer is specified

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  sallybg

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  c078256

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