Changelog • bioseq

Minor changes

Add arguments to write_fasta() to control line and block lengths.
Fix warning message when a non-valid character is automatically replaced by X with AA.
On CRAN request, fix tags/attributes for HTML documentation.

Minor changes

Add support for fuzzy matching in seq_detect_pattern() and seq_crop_pattern().
Fixed missing output in seq_spellout() for collapse = NULL.

Minor changes

Use getOption() instead of options() in function arguments (Functions aliview, seaview, print_sequences, print.bioseq_dna, print.bioseq_rna and print.bioseq_aa).

Bug fixes

Fix bug when importing fasta with > characters in sequence names.
Fix bug when exporting fasta (write_fasta) with NA sequences.

Documentation improvements

On CRAN request, add a reference to Keck (2020) in description.
New logo.
Add CITATION file.

New features

New system to disable colors in the console when printing sequences using global options: options(bioseq.color = "none").
New system to set GUI paths for seaview() and aliview() using global options (bioseq.seaview.exec and bioseq.aliview.exec).

Bug fixes

Fix bug with names when named biological sequences are provided to functions that return a list (seq_extract_pattern, seq_split_pattern, seq_split_kmer).

Documentation improvements

Documentation of seaview() and aliview() was improved to explain the exec arguments.

First version