NEWS.md

In bioseq: A Toolbox for Manipulating Biological Sequences

bioseq 0.1.4

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.

bioseq 0.1.3

Minor changes

• Add support for fuzzy matching in seq_detect_pattern() and seq_crop_pattern().

• Fixed missing output in seq_spellout() for collapse = NULL.

bioseq 0.1.2

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.

bioseq 0.1.1

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.

bioseq 0.1.0

• First version

bioseq documentation built on Sept. 6, 2022, 5:07 p.m.