Changelog

Source: NEWS.md

tidysq 1.2.0

New features:

  • write_fasta() and find_motifs() accept data.frame arguments now; sequences and their names are taken from specified two columns
  • more descriptive error messages for non-existing generics that print out classes of the first parameter

Fixed-ish:

  • return to autoexported Rcpp catch declaration

Quality of code stuff:

  • added tests and adjusted vignettes for the changes

tidysq 1.1.32022-01-31

Fixed:

  • replaced deprecated use of iterator

tidysq 1.1.2-12021-07-27

Fixed:

  • adjusted declaration of function autoexported by Rcpp to match new testthat standards

tidysq 1.1.2

Fixed:

  • early return now works correctly for remove_ambiguous()
  • ensured correct order of operations during sequence packing
  • changed some values to unsigned wherever there was a mismatch

tidysq 1.1.1

Updates for the CRAN god. Fixed random_sq() out-of-bounds possible problem, so there may be differences in sequences generated using the same seed in this and previous versions.

Fixed:

  • upper bound for random_sq() correctly ignores now "*" and “-” values while computing number of letters to draw from
  • removed default move/copy constructors/assignment operators for Sequence and ProtoSequence classes
  • lots of technical files cleanup

tidysq 1.1.02021-03-12

Expanded on v1.0.0, having implemented functions paste() and collapse() that allow the user to connect multiple sequences into one. Also made some optimization within C++ using templates, speeding up translate() and complement() functions significantly. Lastly, added support for object from bioseq package.

Breaking changes:

  • dropped argument interpret_as_stop from translate() function, as it is not feasible to implement well-working translation rules for tables with ambiguous codons (27, 28 & 31)

New features:

  • implemented paste() (a method for sq class)
  • implemented collapse()
  • added support for classes from bioseq package, i.e. bioseq_aa, bioseq_dna and bioseq_rna

Improved:

Fixed:

  • made random_sq() actually use seed parameter while generating sequences

tidysq 1.0.0

Initial stable release.