2019-03-15 - genio 1.0.0.9000

• First GitHub release! Includes read_bim, read_fam, read_ind, and read_snp functions.

2019-03-31 - genio 1.0.1.9000

• Added an efficient write_bed written in Rcpp and thoroughly tested against BEDMatrix package.

2019-04-01 - genio 1.0.2.9000

• Improved write_bed error message for invalid data, documentation.
• Extended write_bed tests.

2019-04-01 - genio 1.0.3.9000

• Added write_fam, write_bim, write_ind, write_snp functions.
• Refactored read_* code, updated docs and tests.

2019-04-02 - genio 1.0.4.9000

• Added make_fam, make_bim, and write_plink functions.
• Fixed read_fam bug (used to require phenotypes to be integers, now can be double numbers).
• Added verbose option to write_bed.

2019-04-05 - genio 1.0.5.9000

• write_plink now returns NULL invisibly.
• Added require_files_plink, delete_files_plink.
• Removed “Fatal:” prefix from stop messages.

2019-04-08 - genio 1.0.6.9000

• Added ind_to_fam, sex_to_int, sex_to_char.
• 2019-05-13: added ORCID to author info

2019-05-16 - genio 1.0.7.9000

• Added read_bed and read_plink! Now all plink reading and writing operations are supported.
• Added package documentation summarizing main read and write functions.
• Added vignette comparing our BED reader and writer to those of BEDMatrix, snpStats, and lfa.

2019-05-21 - genio 1.0.8

• First CRAN submission
• Genotype matrix row and column names from BIM/FAM files
  • read_plink now includes row and column names automatically.
  • read_bed accepts either row and column names or just their numbers.
  • write_plink checks these row and column names against the BIM and FAM tables for consistency, if these are all present.
• Added memory estimation and comparisons sections to vignette.
• Windows debugging
  • Now BED writing is in binary mode, like reading already was.
  • Reduced comparisons to BEDMatrix in testing, since it leaves temporary files open and on Windows they do not get deleted and leave confusing error messages behind.

2019-05-24 - genio 1.0.9

• CRAN-requested edits, resubmission
  • DESCRIPTION edits
  • Changed examples, vignettes, and tests to write files to the default temporary directory.

2019-05-28 - genio 1.0.10

• CRAN submission follow ups, fixing issues that arose on other systems:
  • Added include <cerrno> to my cpp code.
  • Fixed a “heap buffer overflow” detected by valgrind that only occurred for data with fewer than 9 individuals (included many of my toy tests).
  • Edited a test within vignette to allow for small machine precision-level errors.

2019-07-22 - genio 1.0.11

• Added read_phen and write_phen, a phenotype format (very similar to plink’s FAM) used by GCTA and EMMAX.
• Now write_plink returns the data it wrote, invisibly as a list. Most useful for auto-generated data.

2019-08-05 - genio 1.0.11.9000

• Fixed a “buffer overflow” bug that occurred when input files started with “~/” on Unix systems.

2019-12-17 - genio 1.0.12

• Second CRAN submission
• Moved logo to man/figures/
• Minor Roxygen-related updates.