update news and changelog

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",

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.