NEWS
BSgenome 1.80.0
DEPRECATED AND DEFUNCT
- Functions BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg
are now formally defunct in BioC 3.23 after being deprecated in BioC 3.22.
BSgenome 1.78.0
SIGNIFICANT USER-VISIBLE CHANGES
- The package now depends on the new Seqinfo package instead of
GenomeInfoDb.
BSgenome 1.76.0
DEPRECATED AND DEFUNCT
- Formally deprecate BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg.
All these functions are now defined in the BSgenomeForge package.
BSgenome 1.74.0
- No significant changes in this version.
BSgenome 1.72.0
SIGNIFICANT USER-VISIBLE CHANGES
- The vignette documenting the seed-based forging process has moved
to the BSgenomeForge package. This vignette used to be called
the "BSgenomeForge vignette" but it has now be renamed
the "Advanced BSgenomeForge usage" vignette.
- All the tools related to the seed-based forging process and used by
the "Advanced BSgenomeForge usage" vignette are now in the BSgenomeForge
package.
BSgenome 1.28.0
NEW FEATURES
- Add seqnames() setter for BSgenome objects so users can rename
the single sequences in those objects. This has been a popular user
request for a while.
SIGNIFICANT USER-VISIBLE CHANGES
- Add sanity check to "getSeq" method for BSgenome objects, raising an
error if the supplied BSgenome and GRanges objects are based on
incompatible reference genomes.
MISCELLANEOUS
- Started the NEWS file (this file).