Changes in version 0.99.6 - Sept 15, 2026 - update configure.ac Changes in version 0.99.3 - Sept 10, 2026 - remove compute_scale.cpp to pass BioC tests Changes in version 0.99.2 - Sept 10, 2026 - reduce max file size by splitting sqlite3.c - namespace changes to pass Bioc checks Changes in version 0.99.1 - July 8, 2026 - readH5AD() is faster and fixes issue reading raw/var - now just reads var Changes in version 0.99.0 - May 1, 2026 - version bump for Bioc - pass BiocCheck Changes in version 0.1.0 - April 30, 2026 - add dashSVD() and rename PCAstream() to PCAone() - updated readH5AD() to handle raw field - provide headers from pgenlibr 0.5.5 Changes in version 0.0.67 - update readH5AD() Changes in version 0.0.66 - add lzma.h Changes in version 0.0.65 - update definitions of MatrixInfo and DataChunk to enable filtering Changes in version 0.0.64 - add readH5AD() with SingleCellExperiment with file-backed counts Changes in version 0.0.63 - Improve performance with no variant filtering Changes in version 0.0.62 - Fix bugs in PCA, DataChunk and GenomicDataStreamParallel Changes in version 0.0.61 - update Makefile to resolve install issues Changes in version 0.0.60 - June 30, 2025 - Faster PCA for VCF and BCF that solves filtering issue Changes in version 0.0.59 - June 23, 2025 - bgenstream now supports reading a large number of genomic intervals using VariantSet and then querying by rsid instead of postion, instead of crashing at ~10k - In VariantSet, add id field - In pgenstream move where VariantSet is initialized Changes in version 0.0.58 - June 18, 2025 - Article addressing RcppParallel on Mac OS X - Fix Makefile Changes in version 0.0.57 - June 16, 2025 - Fix issue with multiple variants at the same site - PCA is now parallelized with oneTBB - add GenomicDataStreamParallel.h Changes in version 0.0.54 - June 10, 2025 - Move Depends to Imports Changes in version 0.0.53 - June 3, 2025 - PCAstream() works on DelayedArray and SingleCellExperiment - Add scaleAndCenter argument - add compute_center_and_scale() Changes in version 0.0.52 - May 30, 2025 - Update PCAstream() - update C++ streams to add useFilter - in C++, add applyVariantFilter() based on MAF for SNPs - Update DelayedStream - PCAOne works for DelayedStream Changes in version 0.0.51 - May 21, 2025 - Fix bug reading plink files Changes in version 0.0.50 - May 19, 2025 - Fix issue with buffer overflow when reading plink files Changes in version 0.0.40 - May 15, 2025 - Progress on PCAstream() - parsing plink BIM and FAM files supports tab and space delimiters Changes in version 0.0.30 - May 12, 2025 - Add new PCAstream() using stream_pcaone() algorithm with C++ code contributed by @Zilong-Li Changes in version 0.0.20 - April 21, 2025 - Resolve R CMD check Notes - refactor for compatibility across ecosystem Changes in version 0.0.19 - April 4, 2025 - use GabrielHoffman/vcfppR in DESCRIPTION Changes in version 0.0.18 - April 4, 2025 - bug fix in main Changes in version 0.0.17 - March 12, 2025 - add winSVDstream() Changes in version 0.0.16 - Feb 12, 2025 - add MAF / minVariance filter to GenomicDataStream() and backend C++ code - add colnames to coef and se - add getSampleNames() Changes in version 0.0.15 - Feb 5, 2025 - GenomicDataStream can parse genetics file one time, then use setRegion() multiple times to query different regions - changes to vcfstream.h, pgenstream.h, bgenstream.h to allow single initialization and multiple queries with setRegion() multiple times - fix issue with vcfstream::setRegions() failing when empty region was used after a valid region Changes in version 0.0.14 - Jan 30, 2025 - update Makevars.in - get BH v1.84 from eddelbuettel/bh@852b468 Changes in version 0.0.13 - Jan 29, 2025 - remove dependency on Rhtslib Changes in version 0.0.10 - Jan 23, 2025 - update to pgenlibr v0.4.0 - move regression to separate package - remove src/zstd-1.1.0 Changes in version 0.0.9 - Dec 18, 2024 - use fitLinReg 0.0.5 - check BH (== 1.84.0.0) since 1.87.0-1 is not compatible with boost in bgen library Changes in version 0.0.8 - Dec 16, 2024 - bug fixes and convergence criteria Changes in version 0.0.7 - Dec 12, 2024 - add glmFitResponses() and glmFitFeatures() Changes in version 0.0.6 - Dec 3, 2024 - add dependency fastLinReg Changes in version 0.0.5 - Nov 19, 2024 - Improve interface, documentation and integration with fastlmm Changes in version 0.0.4 - Oct 31, 2024 - towards support for pgenlibr Changes in version 0.0.3 - Oct 29, 2024 - DelayedStream fixed - add genetic Datainfo Changes in version 0.0.2 - Oct 24, 2024 - Add support for BGEN 1.x with phased or unphased biallelic variants - test data in inst/extdata/ - extensive testing for multiple file formats - Fix BGEN issue with NaN for unphased data Changes in version 0.0.1 - Sept 29, 2024 - Add support for multiple file types