v0.4.1

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

• Design genomics-first TUI by @nuin in #3

Full Changelog: v0.3.2...v0.4.0

v0.3.2

Full Changelog: v0.3.1...v0.3.2

v0.3.1

Full Changelog: v0.3.0...v0.3.1

v0.3.0

Full Changelog: v0.2.0...v0.3.0

v0.2.0

Full Changelog: v0.1.3...v0.2.0

v0.1.3

Full Changelog: v0.1.2...v0.1.3

v0.1.2

What's Changed

• Revise README for clarity and serverless details by @nuin in #2

New Contributors

• @nuin made their first contribution in #2

Full Changelog: v0.1.1...v0.1.2

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

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.

v0.1.0 — research preview

Initial research preview of vcfclick.

A small VCF databases tool with an embedded ClickHouse engine,
embedded DuckDB annotations, and an MCP natural-language layer.

Quick start

pip install vcfclick

# pull the included 1000 Genomes BRCA1 demo database
vcfclick db pull demo https://github.com/nuin/vcfclick/releases/download/v0.1.0/1000g-brca1-demo.tar.gz

# run a query
vcfclick db query demo "SELECT count(DISTINCT (ingest_id, sample_id)) AS n_samples FROM genotypes WHERE chrom='chr17' AND pos BETWEEN 43044295 AND 43170245"

Assets

• 1000g-brca1-demo.tar.gz — a ready-to-use vcfclick database bundle
  (1000 Genomes Phase 3 30x BRCA1 region, 3,014 variants × 3,202 samples).
  Restore with vcfclick db pull <name> <url>.
• vcfclick-0.1.0-py3-none-any.whl — Python wheel.
• vcfclick-0.1.0.tar.gz — source distribution.

Benchmark

End-to-end on a 1000 Genomes chr17 10Mb slice (235,768 variants ×
3,202 samples = 44.99M sparse calls), vcfclick parallel-8 ingests in
69s — ~70× faster than the comparable TileDB-VCF workflow. Full
methodology and caveats in bench/BENCHMARK.md.