openvax / varcode / 25612627701
88%

DEFAULT BRANCH: main
Ran
Jobs 0
Files 0
Run time –
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
25612627701

push

github

web-flow 
Audit docs and README: remove ASCII flowcharts, defrost stale roadmap claims, refresh public surface (#362)

User-flagged ASCII flowcharts in docs/germline.md and docs/effect_annotation.md
replaced with prose. Both diagrams overstated their explanatory value
and don't reproduce well in narrow viewports.

Stale roadmap-y claims removed where the work has shipped:

- effect_annotation.md described ProteinDiffEffectAnnotator as
  '#309 — WIP' but it's been the default since 4.18; now lists all
  three annotators (protein_diff, fast, structural_variant) with their
  actual selection rules.
- effect_annotation.md's 'Structural variants (roadmap)' section
  described unimplemented work; #357 shipped end-to-end SV loading
  and annotation. Replaced with a working-feature description and
  the few real remaining limitations (mate breakend pairing,
  parse_structural_variants=False default).
- effect_annotation.md's splice section had ~100 lines explaining the
  relationship between ExonicSpliceSite and SpliceOutcomeSet; trimmed
  to the essential table + one paragraph. Same content, half the words.
- effect_annotation.md's 'Downstream consumers' section was a roadmap
  for topiary/vaxrank/isovar consumption; replaced with a brief note
  pointing at the resolver pattern in germline.md.
- genotype.md's 'What this doesn't do yet' listed phased effects
  (#269) and germline-aware (#268) as deferred; both have shipped.
  Replaced with a 'Beyond zygosity' section pointing at the live
  features.
- csv.md dropped the '(tracked in #271)' parenthetical — #271 is
  closed.

Public-surface gaps filled:

- docs/index.md links the germline guide.
- README.md replaces the stale Further-reading list with the
  current set (effect annotation, germline, genotypes, CSV, errors)
  and points at the live docs site. Coverage badge URL fixed
  (master → main).
- docs/api.md adds entries for everything new since the existing
  list was written: StructuralVariant, parse_symbolic_alt... (continued)
Source Files on build 25612627701
Detailed source file information is not available for this build.