diff --git a/DESCRIPTION b/DESCRIPTION index 6b869af..c8c7f99 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: tidysq Type: Package Title: Tidy Processing and Analysis of Biological Sequences -Version: 1.2.0 +Version: 1.2.1 Date: 2022-01-29 Authors@R: c(person("Dominik", "Rafacz", email = "dominikrafacz@gmail.com", diff --git a/NEWS.md b/NEWS.md index 99140f6..13af3c1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,53 +1,59 @@ -# 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 1.1.3 -## 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 1.2.1 + +## Fixed: +* fixed incorrect codons +* add explicit casting of alphabet during construction of sequence prototype (fixes issues with new implementation of `union()`) + +# 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 1.1.3 +## 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.