NEWS

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GenomicDataStream 0.99.6

• Sept 15, 2026
• update configure.ac

GenomicDataStream 0.99.3

• Sept 10, 2026
• remove compute_scale.cpp to pass BioC tests

GenomicDataStream 0.99.2

• Sept 10, 2026
• reduce max file size by splitting sqlite3.c
• namespace changes to pass Bioc checks

GenomicDataStream 0.99.1

• July 8, 2026
• readH5AD() is faster and fixes issue reading raw/var
  • now just reads var

GenomicDataStream 0.99.0

• May 1, 2026
• version bump for Bioc
• pass BiocCheck

GenomicDataStream 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

GenomicDataStream 0.0.67

• update readH5AD()

GenomicDataStream 0.0.66

• add lzma.h

GenomicDataStream 0.0.65

• update definitions of MatrixInfo and DataChunk to enable filtering

GenomicDataStream 0.0.64

• add readH5AD() with SingleCellExperiment with file-backed counts

GenomicDataStream 0.0.63

• Improve performance with no variant filtering

GenomicDataStream 0.0.62

• Fix bugs in PCA, DataChunk and GenomicDataStreamParallel

GenomicDataStream 0.0.61

• update Makefile to resolve install issues

GenomicDataStream 0.0.60

• June 30, 2025
• Faster PCA for VCF and BCF that solves filtering issue

GenomicDataStream 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

GenomicDataStream 0.0.58

• June 18, 2025
• Article addressing RcppParallel on Mac OS X
• Fix Makefile

GenomicDataStream 0.0.57

• June 16, 2025
• Fix issue with multiple variants at the same site
• PCA is now parallelized with oneTBB
• add GenomicDataStreamParallel.h

GenomicDataStream 0.0.54

• June 10, 2025
• Move Depends to Imports

GenomicDataStream 0.0.53

• June 3, 2025
• PCAstream() works on DelayedArray and SingleCellExperiment
• Add scaleAndCenter argument
• add compute_center_and_scale()

GenomicDataStream 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

GenomicDataStream 0.0.51

• May 21, 2025
• Fix bug reading plink files

GenomicDataStream 0.0.50

• May 19, 2025
• Fix issue with buffer overflow when reading plink files

GenomicDataStream 0.0.40

• May 15, 2025
• Progress on PCAstream()
• parsing plink BIM and FAM files supports tab and space delimiters

GenomicDataStream 0.0.30

• May 12, 2025
• Add new PCAstream() using stream_pcaone() algorithm with C++ code contributed by @Zilong-Li

GenomicDataStream 0.0.20

• April 21, 2025
• Resolve R CMD check Notes
• refactor for compatibility across ecosystem

GenomicDataStream 0.0.19

• April 4, 2025
• use GabrielHoffman/vcfppR in DESCRIPTION

GenomicDataStream 0.0.18

• April 4, 2025
• bug fix in main

GenomicDataStream 0.0.17

• March 12, 2025
• add winSVDstream()

GenomicDataStream 0.0.16

• Feb 12, 2025
• add MAF / minVariance filter to GenomicDataStream() and backend C++ code
• add colnames to coef and se
• add getSampleNames()

GenomicDataStream 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

GenomicDataStream 0.0.14

• Jan 30, 2025
• update Makevars.in
• get BH v1.84 from eddelbuettel/bh@852b468

GenomicDataStream 0.0.13

• Jan 29, 2025
• remove dependency on Rhtslib

GenomicDataStream 0.0.10

• Jan 23, 2025
• update to pgenlibr v0.4.0
• move regression to separate package
• remove src/zstd-1.1.0

GenomicDataStream 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

GenomicDataStream 0.0.8

• Dec 16, 2024
• bug fixes and convergence criteria

GenomicDataStream 0.0.7

• Dec 12, 2024
• add glmFitResponses() and glmFitFeatures()

GenomicDataStream 0.0.6

• Dec 3, 2024
• add dependency fastLinReg

GenomicDataStream 0.0.5

• Nov 19, 2024
• Improve interface, documentation and integration with fastlmm

GenomicDataStream 0.0.4

• Oct 31, 2024
• towards support for pgenlibr

GenomicDataStream 0.0.3

• Oct 29, 2024
• DelayedStream fixed
• add genetic Datainfo

GenomicDataStream 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

GenomicDataStream 0.0.1

• Sept 29, 2024
• Add support for multiple file types