NEWS

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tidyGenR 0.1.8

• fixed compare_calls(), did not allow creads = T in "genotypes".
• new function align_variants_ref() runs pairwise alignments with local reference sequences and attaches alignment stats to tidy variants. Useful to spot homologous/non-homologous variants.

tidyGenR 0.1.7 (2026-02-17)

• fixed CRAN checks: tempdir and tempfiles for examples and tests, remove examples for internal ::: functions, add @value where missing.
• remove unused data objects msa and qlist.

tidyGenR 0.1.6

• first submission to CRAN.
• trunc_amp(), includes 'filt_name' argument to add flexibility to output filtered names.
• x-axis scale has changed in 'explore_dada()'
• optimization vignette added.
• 'out_popart()' internal 'write_delim(quote)' changed to "none".
• replace absolute paths by temp paths in examples.

tidyGenR 0.1.5

• bug fixed in 'variant_call_dada()', dada2 is always converted to list to prevent errors associated to loci in one sample only.

tidyGenR 0.1.4

• 'demultiplex(mode = 'linked')' has been tested with real data. The R primers needed to be reverse-complemented. Fixed.

tidyGenR 0.1.3

• updated 'gen_wide2genalex()'. 'tidyr::separate_wider_delim()' replaced with base R code.
• 'ploidy' attribute is kept for remove_hemizygotes

tidyGenR 0.1.2

• updated 'gen_wide2structure()'. 'tidyr::separate_longer_delim()' could not handle correctly NA's and the code was replaced with base R.
• 'ploidy' attribute is kept for genotype conversions.

tidyGenR 0.1.1

• Update NEWs and README.

tidyGenR 0.1.0

Initial Release

• Core functions available.
• Clean .git.
• Stable version.
• Old .git was removed and fresh .git was initiated after checking the rcmdcheck did not return any error.