NEWS

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tidysq 1.2.1 (2024-10-06)

Fixed:

• fixed incorrect codons
• add explicit casting of alphabet during construction of sequence prototype (fixes issues with new implementation of union())
• add skips for tests that use not available packages from "Suggests"

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:

• return to automatically exported Rcpp catch declaration

Quality of code stuff:

• added tests and adjusted vignettes for the changes

tidysq 1.1.3 (2022-01-31)

Fixed:

• replaced deprecated use of iterator

tidysq 1.1.2-1 (2021-07-27)

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 1.1.0 (2021-03-12)

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:

• remade translate() to have codon tables created in compile time; this reduced execution time of translate() by 95%
• remade complement() to have tables created in compile time; this reduced execution time of complement() by 85%

Fixed:

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

tidysq 1.0.0

Initial stable release.