teaguesterling/plinking_duck v0.10.0

v0.10.0 — Phase-2 reader capabilities + pfile writer

on GitHub

plinking_duck v0.10.0 combines two reviewed feature tracks: the Phase-2 reader capabilities and the pfile writer.

Phase-2 reader capabilities

• with_ordinal / __ordinal — opt-in stable per-file row ordinal on the readers.
• pfile_partitions() — table function that enumerates partition ranges for a pfile, with variant_range now accepted on read_pfile for bounded reads.
• plinking_duck_capabilities() — scalar that reports the build's live capabilities, derived from the real catalog.
• Catalog-visible named parameters — table-function named params now render by their real names in duckdb_functions(), and a curated param is required on every reader overload.

pfile WRITER

• COPY … TO (FORMAT pfile | pvar | pgen | psam) — write PLINK2 filesets from DuckDB.
• Full read → write → read round trip.
• Atomic writes (staging + promote; no partial filesets left on failure).
• Explicit-identity .psam output.
• Local-only destinations, biallelic hardcalls.

Honest deferrals (not in this release)

• Per-sample metadata beyond IID.
• Phased genotypes and dosages.
• Multiallelic allele-identity on write.
• Parquet output, .pgi index, sharded output, and PLINK→VCF conversion.

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