docs: add genvarloader public-API skill#174
Merged
Merged
Conversation
Adds skills/genvarloader/SKILL.md, an AI-agent reference for gvl's public Python API covering bcftools/plink2 preprocessing, SVAR vs BCF/PGEN trade-offs, gvl.write and Dataset.open arguments, with_seqs/with_tracks/ with_len modes, the five insertion-fill strategies, spliced haplotypes, site-only variants, and pointers into docs and source for deeper detail. CLAUDE.md gains a maintenance rule: PRs changing the public API (__all__, gvl.write, Dataset.open, Dataset.with_*) must also update the skill. Skill is distributed via skills.sh as mcvickerlab/GenVarLoader (npx skills add mcvickerlab/GenVarLoader). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
d-laub
force-pushed
the
docs/genvarloader-skill
branch
from
d86b8dc to
1af3f54
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
skills/genvarloader/SKILL.md— an AI-agent reference for gvl's public Python API: bcftools/plink2 preprocessing, SVAR vs BCF/PGEN,gvl.write/Dataset.open/Dataset.with_*, the five insertion-fill strategies, spliced haplotypes, site-only variants, and pointers intodocs/and source for deeper detail.CLAUDE.md: public-API changes (anything in__init__.py's__all__, plusgvl.write/Dataset.open/Dataset.with_*signatures and defaults) must update the skill in the same PR.npx skills add mcvickerlab/GenVarLoader) — the repo-rootskills/<name>/SKILL.mdlayout is what their CLI expects.Why
Cold use of gvl is harder than it should be: a baseline subagent asked to build a haplotype + track + splice script from scratch (no skill, source-only) got stuck on SVAR vs BCF/PGEN trade-offs, valid
with_seqs/with_tracksliterals, insertion-fill discoverability, and thesplice_infotuple form. The skill documents exactly those decision points and points to canonical docs for the rest.Test plan
🤖 Generated with Claude Code