feat: fixes for next Bioc release #118
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Major changes:
- new workflow file to run tests
- numerous unit tests
Minor changes:
- warning in translate.R:16 has been elevated to an error because AA_ALPHABET is now enforced.
error messages for letter.R are standardized, some additional error checking is added.
- mask was scheduled to be deprecated in Biostrings 2.9. This function now throws a warning when it is used and will be removed in a subsequent release.
man/XStringSetList-class.Rd previously said that "DNAStringSetList and AAStringSetList are the only constructors", but the current version of Biostrings includes BStringSetList and RNAStringSetList constructors. This has been updated.
- Some tests were included inline in replaceAt.R wrapped in if(FALSE){...} brackets. These have been moved to the unit tests, and performance/timing tests have been removed.
- replaceAmbiguities now checks to ensure input is one of DNAString, RNAString, or the XStringSet/XStringSetList analogs. This previously caused some odd behavior with input of type AAString.
- an erroneous extra (useless) argument to make_AA_COLORED_LETTERS has been removed.
- a warning in XStringViews-class.R that was supposed to be suppressed in Bioc 2.12 has been suppressed.
- tests in inst/unitTests have been ported to testthat when possible. Accordingly, run_unitTests.R has been removed.
- Some files have had trailing whitespace removed.
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This is a combination of all open PRs for Hervé's approval prior to final merge into
devel. Each commit will be added here with a link to the previous PR. Expected to merge following 3.20 release.consensusString,consensusMatrix(PR 111)readQualityScaledXStringSet(PR 110)