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Commits on Feb 20, 2025

• Internal function `add_ext_read` (affects `count_lines`, `het_reencode_bed`, and probably all or most `read_*` functions) now works as intended when the file without extension matches a directory n…

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Commits on Feb 7, 2025

• Modernized `Rcpp` code to use standard C++ library, avoiding various pitfalls and making code shorter and more readable!

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Commits on Aug 24, 2024

• Added function `symlink`, package dependency `R.utils`, and function `het_reencode_bed` added option `make_bim_fam`

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Commits on Aug 22, 2024

• Added function `het_reencode_bed`

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• Function `write_bed_cpp` corrected variable names (had `n_ind` and `m_loci` reversed), and added wide genotype matrix (`n_ind > m_loci`) to unit tests

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Commits on Feb 28, 2024

• Added function `sim_and_write_plink`

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Commits on Jan 5, 2023

• Fixed an R-devel warning by removing all `sprintf` calls in Rcpp code; prepped for cran submission

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Commits on Sep 15, 2022

• Function `write_plink` added option `write_phen`

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Commits on Apr 27, 2022

• added CRAN-SUBMISSION to .Rbuildignore (done automatically by devtools::release)

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• non-code updates for 5th CRAN submission

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Commits on Apr 20, 2022

• Functions `read_bim`, `write_bim`, and `geno_to_char`: reversed columns "ref" and "alt" in BIM table

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Commits on Feb 2, 2022

• Function `write_bed` now checks if output directory exists prior to attempting to open the file for writing in the C++ part of the code; closes #6

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Commits on Jan 28, 2022

• read_grm minor doc updates

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• `write_grm` extended to write "plink2 --make-king" style outputs

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• `read_grm` added options to parse outputs from `plink2 --make-king bin` and variants

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Commits on Jan 14, 2022

• bugfix in add_ext_read (and its read_* dependencies): Now setting `ext = NA` finds files that end in a `.gz` extension that was not specified (before those files were incorrectly not found)

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Commits on Aug 18, 2021

• Functions `read_eigenvec` and `write_eigenvec` have new option `plink2` for better handling files with headers in the default style of plink2.

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Commits on Aug 17, 2021

• applied same `path.expand` fix to `count_lines` to expand "~/"

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• Functions `write_bed` and `write_plink` fixed a bug: write failed if output path started with "~/" on Unix systems.

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Commits on Aug 13, 2021

• Function `read_eigenvec` fixed a warning about tibble

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Commits on Jul 26, 2021

• write_bed with append=TRUE debugged; replaced readr::read_table2 with read_table (closes #4); replaced pryr::object_size with lobstr::obj_size (fixed vignette error)

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Commits on Jul 1, 2021

• Functions `read_bed` and `read_plink` no longer stop with an error if the input BED file has non-zero padding bits; closes #3

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• Function `read_bed` now reads `file` even if it doesnt have a BED extension (as long as it exists), added `ext` option; closes #2

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Commits on Jun 11, 2021

• minor edits in prep for CRAN resubmission

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Commits on May 21, 2021

• Function `count_lines` now returns value as integer instead of double

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Commits on Apr 27, 2021

• added functions `read_matrix` and `write_matrix`

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• added function `geno_to_char`

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Commits on Feb 16, 2021

• documentation updates: GRM examples in README and package doc, clarifications, full conversion to markdown, spell check

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Commits on Dec 23, 2020

• function read_bed added missing file check in R code to override C++ check that was suceptible to buffer overflow

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• vignette removed lfa comparison

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Commits on Aug 17, 2020

• read_eigenvect added plink2 support via `comment = "#"` option

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Commits on Jul 31, 2020

• forgot to remove iterators version from runtime eval

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• count_lines made iterators C++ version the default (deleted other version), as it was fastest on huge files

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• added count_lines, including two C++ backends (count_lines_cpp and count_lines_iterators_cpp) that pass tests

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Commits on Jul 28, 2020

• added read_eigenvec

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