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Changelog

Source: NEWS.md

RGlimpse2 0.0.0.9003

  • Include the pthread header directly in threaded native callers so Rtools ARM64 builds do not depend on a transitive header.

RGlimpse2 0.0.0.9002

  • Preserve biallelic symbolic and ambiguous reference records during direct-BAM phasing without attempting a read-level call, and declare GP with VCF Number=G for ploidy-correct likelihood cardinality.

RGlimpse2 0.0.0.9001

  • Add rglimpse2_phase_bam() for deterministic direct phasing and imputation from one explicitly indexed BAM or CRAM.

  • Add rglimpse2_phase_bams() for one native multi-sample GLIMPSE2_phase --bam-list call with explicit indexed alignments, sample names, and mixed haploid/diploid ploidy. Private BAM/ploidy tables are removed after the call, and the BCF plus its CSI index are published without replacement only after successful staging.

  • Make rglimpse2_split_reference() return a typed non_biallelic_reference input error before starting GLIMPSE2 when the requested reference region contains unsplit records.

  • Keep biallelic symbolic and other non-observable reference variants in direct-BAM imputation with flat read likelihoods instead of routing them through the SNP caller.

  • Ligate overlapping all-haploid chunks using the one-value-per-sample GT stride returned by HTSlib while preserving mixed and diploid phase matching.

  • The R package interface is now distributed under GPL-2 or later; bundled upstream components retain their original licences and notices.

  • Give every typed operational error the same optional child-process operation and status properties. This preserves the error-value contract when binary build systems install and check separate copies of the package.

  • Add a nested R package that builds pinned GLIMPSE2 chunk, split-reference, phase, and ligate executables against the validated htslib contract supplied by Rduckhts.

  • Bundle the pinned GRCh37 and GRCh38 autosomal and chromosome X genetic maps, plus explicit zero-recombination coordinate maps for Y non-PAR and mitochondrial sequence, with audited lookup helpers and provenance. Map lookup accepts chromosome names with or without chr and treats M, MT, chrM, and chrMT as mitochondrial aliases.

  • Handle zero-span maps safely in phase PBWT grouping. Replace executable test doubles with reproducible vcfppR-generated BCF reference/target pairs that run the real chunk, split-reference, phase, and ligate executables across autosomal, Y, and mitochondrial contig aliases.

  • Add stateless wrappers with explicit paths, arguments, seeds, and resources; typed S7 results and operational errors; and typed contract conditions. Split-reference coordinates are canonicalized before output prediction, output paths must be distinct, and ligate lists are validated exactly as the native reader consumes them. Child executables are launched directly with processx argument vectors without an intermediate shell command.

  • Build scalar and architecture-specific phase executables and select only runtime-supported AVX2, AVX-512F/BW/VL, or NEON backends.

  • Add Unix and Rtools configure paths, pinned SIMDe headers, source-archive drift auditing, and a checksummed Boost 1.90.0 build-only source closure so the executables no longer depend on separately installed Boost headers or libraries. Use parallel native compilation with 2–8 detected make jobs, real executable help/linkage tests, and a synthetic native end-to-end conformance test across all supported SIMD backends.

  • Add pkgdown configuration, package-development targets, release checks for Linux, macOS, and Windows, and Linux R-devel coverage. WebAssembly installs retain map and metadata APIs but explicitly omit GLIMPSE2 child executables because that runtime cannot launch the required native processes.