genio 1.0.0.9000 (2019-03-15)

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

genio 1.0.1.9000 (2019-03-31)

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

genio 1.0.2.9000 (2019-04-01)

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

genio 1.0.3.9000 (2019-04-01)

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

genio 1.0.4.9000 (2019-04-02)

• 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.

genio 1.0.5.9000 (2019-04-05)

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

genio 1.0.6.9000 (2019-04-08)

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

genio 1.0.7.9000 (2019-05-16)

• 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.

genio 1.0.8 (2019-05-21)

• 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.

genio 1.0.9 (2019-05-24)

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

genio 1.0.10 (2019-05-28)

• 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.

genio 1.0.11 (2019-07-22)

• 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.

genio 1.0.11.9000 (2019-08-05)

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

genio 1.0.12 (2019-12-17)

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

genio 1.0.13 (2020-05-21)

• Added tidy_kinship to transform a square symmetric matrix into a long-format table that is easy to sort and add annotations to

genio 1.0.13.9000 (2020-06-16)

• Added read_grm and write_grm to read and write GCTA’s binary genetic relatedness matrix (GRM) format.
• Also added auxiliary functions require_files_grm, delete_files_grm, require_files_phen, and delete_files_phen.

genio 1.0.14.9000 (2020-06-23)

• Improved error message in validate_tab_generic.

genio 1.0.15.9000 (2020-07-03)

• Functions write_plink, write_bed, and write_bim now have append option, for writing extremely large files in parts.

genio 1.0.16.9000 (2020-07-28)

• Added write_eigenvec and read_eigenvec to read and write Plink/GCTA eigenvector files.

genio 1.0.17.9000 (2020-07-31)

• Added count_lines, uses C++ code (via Rcpp) to count file lines extremely quickly. Intended for counting numbers of individuals (from FAM and equivalent files) or numbers of loci (from BIM and equivalent files) when these files are extremely large and no other information is needed from those files.

genio 1.0.18.9000 (2020-08-17)

• Function read_eigenvec added Plink 2 support via comment option, which by default now treats data after # as comments. This enables automatically parsing eigenvec files generated by Plink 2, whose header line starts with # (this header is ignored). Previously, parsing Plink 2 eigenvec files generated warnings and resulted in the first row being an additional row with all NA values.

genio 1.0.19.9000 (2020-12-22)

• Function read_bed added a missing file check in R code.
  • A check in the underlying C++ code already existed, but it could suffer from a buffer overflow if the erroneous file path was very long. Such buffer overflows are now completely avoided.
• Vignette: Removed lfa comparison.
  • My latest lfa fork doesn’t have function read.bed anymore, previously the slowest and most memory-hungry competitor, which genio::read_plink was being compared to.

genio 1.0.20.9000 (2021-02-16)

• Documentation updates:
  • Added GRM examples to README and genio package doc
  • Clarified language and code examples throughout, normalized style (full conversion to roxygen markdown, including fixing some cases where old non-markdown notation did not work anymore)
  • Spellchecked package

genio 1.0.21.9000 (2021-04-27)

• Added function geno_to_char to convert genotype numeric codes (allele dosages such as 0, 1, 2) into character codes such as ‘A/A’, ‘A/G’, ‘G/G’ (depending on locus).
• Added functions read_matrix and write_matrix, intended for admixture inference data.
• Fixed documentation for read_bed, which previously incorrectly stated that the numerical genotypes (allele dosages) counted alternative alleles (allele 2 in BIM table), whereas the truth is that they count reference alleles (allele 1).

genio 1.0.22.9000 (2021-05-21)

• Function count_lines now returns value as integer instead of double (a very minor bug/annoyance fix).

genio 1.0.23 (2021-06-11)

• 3rd CRAN submission
• Removed lfa from suggested packages (no connection anymore since lfa comparison was removed from vignette in version 1.0.19.9000).
• Fixed a dead link in the vignette.
• Removed “LazyData: true” from DESCRIPTION (to avoid a new “note” on R-devel).

genio 1.0.23.9000 (2021-07-01)

• Function read_bed now reads file even if it doesn’t have a BED extension (as long as it exists).
  • For additional flexibility, this function also has a new ext option.
  • Thanks to Richel Bilderbeek for reporting this problem.
• Updated documentation for some read_* functions to clarify behavior regarding file and ext options.
• Internal changes
  • Renamed internal function real_path to add_ext_read to make the distinction clearer to add_ext.
  • Verified that all read_* functions use add_ext_read while all write_* functions use add_ext. Only function count_lines switched from add_ext to add_ext_read (in addition to read_bed, which led to the earlier change), but count_lines didn’t have a default extension so this change is less likely to matter.
• Reformatted this NEWS.md slightly to improve its automatic parsing.

genio 1.0.24.9000 (2021-07-01)

• Functions read_bed and read_plink no longer stop with an error if the input BED file has non-zero padding bits.
  • A real-life example (link below, also part of tests now) reported by Richel Bilderbeek (Thanks!) caused the error.
  • https://github.com/kausmees/GenoCAE/tree/master/example_tiny
  • I verified that both the plink2 binary and the BEDMatrix R package load this file without complaining about the non-zero pads, so I decided to agree in that behavior. I verified that genio’s data agrees with BEDMatrix after the fix.

genio 1.0.25 (2021-07-26)

• 4rd CRAN submission
• write_bed/plink with append = TRUE debugged to write in “binary” mode.
  • Fixed rare error observed in Windows only, where “binary” mode makes a difference, and only when written bytes matched certain special characters (such as newlines).
  • Bug probably present since append option was introduced in 1.0.15.9000 (2020-07-03).
• Internally replaced readr::read_table2 with readr::read_table
  • Fixes warning message: read_table2() was deprecated in readr 2.0.0. Please use read_table() instead.
    • Reported by Richel Bilderbeek (thanks again!)
  • Requires readr (>= 2.0.0, already on CRAN).
  • Added tests for verbosity
• Replaced pryr::object_size with lobstr::obj_size (a suggested package used in vignette only; the former was recently superseded by the latter)
  • One-line vignette update for a change in former pryr::object_size output (now of class lobstr_bytes), which triggered a CRAN warning.