NEWS.md

In tidysq: Tidy Processing and Analysis of Biological Sequences

tidysq 1.2.3

Fixed:

• Adjusted inner workings of alphabet subsetting in case of non-numeric parameter (fixes #99).

tidysq 1.2.2

Fixed:

• Using unsigned LenSq in loops.

tidysq 1.2.1

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

Fixed:

• replaced deprecated use of iterator

tidysq 1.1.2-1

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

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.

tidysq documentation built on April 12, 2025, 1:37 a.m.