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Changelog

Source: NEWS.md

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

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 0.0.6

  • 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