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v0.1.1 — FORMAT routing fix, discover, ClinVar loader

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@nuin nuin released this 03 Jun 05:03
· 75 commits to main since this release
v0.1.1
b52a1bc

What's new

  • Fix: FORMAT field routing — PL was silently dropped and DP/AD silently NULL when FORMAT column ordering varied between records in the same VCF. Users with multi-record FORMAT diversity were losing data without knowing it. Re-ingest after upgrading to recover the dropped fields.
  • New: vcfclick discover <vcf> — previews which INFO/FORMAT fields land in typed columns vs info_extra / format_extra, with suggested promotion DDL. No ingestion needed.
  • New: vcfclick annotations load-clinvar — pulls the NCBI ClinVar weekly VCF and populates the embedded DuckDB so the MCP clinvar_lookup tool returns real significance calls (was stubbed in 0.1.0).
  • New: bench/run.sh — reproducible ingest benchmark against the 1000G chr17:40-50M slice.
  • New: examples/brca1-cohort.md — worked MCP session with verbatim SQL and chDB outputs against the demo bundle.
  • 29 new tests; suite is now 35 tests covering ingest routing, discover, and the ClinVar loader.

Install / upgrade

```
pip install --upgrade vcfclick
```

The v0.1.0 `1000g-brca1-demo.tar.gz` release asset is still valid; no re-download needed.

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