Named the Rfmalloc sibling explicitly in Remotes, so dependency installers
distinguish its monorepo subdirectory from other packages at the same commit.
Fixed webR builds by classifying wasm32 separately from 32-bit x86 and using
pgenlib's word-width-correct scalar path instead of including xmmintrin.h.
The floating-point setup also stops treating every non-x86 target as arm64.
Removed the unused C-callable API counter. Rpgen and every native consumer evolve together in this monorepo, so the installed header describes one current contract without compatibility branches.
Added rpgen_ingest() as the single composition point for PGEN, PLINK 1
BED, PED/MAP, TPED/TFAM, VCF/BCF, BGEN, Oxford GEN, HAPS/legend,
EIGENSTRAT, and legacy PLINK 1 dosage. Destinations include packed
hardcalls, fixed-point dosage, locus-major haplotypes, and file-backed
full-precision dosage.
PGEN and BED now use one persistent pgenlib reader and bounded variant panels. The panels enter Rfmalloc through a typed record-buffer context, so readers no longer construct a complete genotype matrix or know the destination codec layout.
Added strict phase-preserving reads through PgrGetP(). Phased calls are
written directly to Rfmalloc's locus-major haplotype store. Missing genotypes
and unphased heterozygotes are rejected instead of being silently invented.
Reused PLINK 2's import closure for VCF, BCF, BGEN, GEN, HAPS, PED/MAP,
TPED/TFAM, EIGENSTRAT, and legacy dosage. rpgen_ingest() now redirects
every STPgenWriter append shape into the Rfmalloc record sink, eliminating
temporary PGEN serialization and read-back. File-producing
rpgen_import_*() calls remain unchanged. PED/MAP retains only the bounded
transpose scratch required to change sample-major input into locus-major
output. Direct imports report record transfer instead of claiming that a
nonexistent PGEN was written.
Added fixture-backed round trips for every supported source, including both BGEN layouts, fractional legacy dosage, exact HAPS phase, missing VCF calls, phased multiallelic VCF, packed EIGENSTRAT, PLINK 1 PED/TPED layouts, and comparison with pgenlibr where available.