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Bioconductor Changlog.
Tue, 13 Oct 2009
BSgenome
Moved GenomeData and GenomeDataList to the new TypedListV2 framework.
BSgenome
Added the 'type' arg to the available.SNPs() function. Renamed SNPlocs_pkg() -> SNPlocs_pkgname() and the 'SNPlocs_pkg' arg of injectSNPs() -> 'SNPlocs_pkgname'. Improved error handling in SNPcount() and SNPlocs(). Small improvement to man/injectSNPs.Rd
some improvements to the injectSNPs() code + related utilities, and to their documentation
maskList parameter in the BSParams class no longer a toggle.
This slot now holds a named logical vector that can specify whichever
of the masks you care to change the status of.
BSgenome
Scrap the BSgenomeID class, at least for now. Add some constructors
for the GenomeData(List) classes.
BSgenome
Following renaming of the BStringViews class -> XStringViews in Biostrings. Bumped version to 1.7.8.
BSgenome
fixed small bug in documentation.
BSgenome
Make chrom and genome arguments optional for GenomicRanges. Bump version.
removed quotes from do.call
BSgenome
added seed file for BSgenome.Rnorvegicus.UCSC.rn4
added seed file for BSgenome.Btaurus.UCSC.bosTau3
some adjustments to the BSgenomeForge code in order to properly support extraction of all the AGAPS masks from a single file (needed at least for BSgenome.Ptroglodytes.UCSC.panTro2 so far)
added seed file for BSgenome.Ggallus.UCSC.galGal3
added seed file for BSgenome.Ptroglodytes.UCSC.panTro2
Adds a maskList toggle to bsapply.
added seed file for BSgenome.Hsapiens.UCSC.hg17
got rid of unload() (not needed anymore)
Improved the caching mechanism: now a sequence is automatically removed from the cache at garbage collection if it's not in use anymore (i.e. if there are no other reference to it than the reference stored in the cache). With options(verbose=TRUE), a message will be printed each time a sequence is removed from the cache. Kept unload() for now but it might go away at some point. bsapply() should not deal with caching anymore (no more calls to unload()). Bumped version to 1.9.17.
BSgenome
The "show" method for BSgenome objects now honors the global "width" option. Version bump.
BSgenome
checked in a first version of the BSgenomeForge vignette
BSgenome
More improvements to the BSgenomeForge code. No version bump.
BSgenome
Added the 'strand' argument to "getSeq" method for BSgenome objects.
Bumped version to 1.13.6
BSgenome
Adding aliases to the BSParams man page.
BSgenome
small simplification in plotGenomeHits() by using seqlengths()
Sync up with last changes in IRanges.
BSgenomeForge improvements:
- added support for a single big file .out file containing
the RM information for all the chromosomes together,
- added support for a single big file .bed file containing
the TRF information for all the chromosomes together.
Bumped version to 1.11.1
BSgenome
Add TODO list.
Add some missing docs related to GenomicRanges/GenomicData
Tweak to strand() accessor, now that we support non-numeric storage.
BSgenome
Changed compressible slot name in TypedList to compress to better reflect its purpose now.
BSgenome
Use Views() instead of deprecated views(). Bumped version to 1.9.11
BSgenome
Updated dependents of IRanges to reflect changes in List/ListLike classes.
BSgenome
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
typo
BSgenome
Rewrote the getSeq() function: added the 'width' argument to it, replaced the 'as.XStringViews' arg by the 'as.character' arg, dropped support for 'start' or 'end' of length > 1, enhanced the function to make it extract sequences from the multiple sequences objects contained in the BSgenome object (as suggested by Matt Settles at BioC 2008), and updated and completed its man page. Bumped version to 1.11.3
BSgenome
updated version
export gdApply
BSgenome
masknames() now returns NULL on a BSgenome object with no built-in masks. Updated the GenomeSearching vignette (Masking section). Bumped version to 1.9.15
added the masknames() accessor for BSgenome objects
The BSgenome forge now gives normalized names ("AGAPS", "AMB", "RM", "TRF") to the built-in masks. Bumped version to 1.9.14
fixed problem with error reporting code of the new delayed-loading mechanism
By default, seqlengths.rda and masks.*.rda are now located in the extdata/ folder of a BSgenome data package. Windows binary BSgenome data packages are broken if they are in data/ (they are put in a single RData.zip file when the binary is built).
BSgenome
Move the genome-themed RangedData wrappers to rtracklayer.
BSgenome
masknames() now returns NULL on a BSgenome object with no built-in masks. Updated the GenomeSearching vignette (Masking section). Bumped version to 1.9.15
BSgenome
updated version
changed show() method to use IRanges:::labeledLine instead of copy/paste
added gdapply, deprecated gdApply
Changed bsapply function to return a GenomeData (TypedList) object when simplify = FALSE.
BSgenome
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
BSgenome
Fixed injectSNPs() so loading a sequence for which no SNPs are available doesn't produce an error anymore. Version bump.
Added the available.SNPs() utility function for getting the list of SNPlocs.* packages currently available + the "SNPlocs_pkgname" accessor for BSgenome objects + the injectSNPs() function for injecting SNPs into a BSgenome object. Version bumped.
BSgenome
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
added missing doc
BSgenome
Some improvements to the BSgenomeForge code. Version bumped to 1.9.2
BSgenome
Updated dependents of IRanges to reflect changes in List/ListLike classes.
BSgenome
Further clean up of strand methods.
Moved strand method for RangedData out of rtracklayer and into BSgenome as a method for DataTable.
BSgenome
added seed file for BSgenome.Hsapiens.UCSC.hg18
added a (template) man page for the data sets included in a BSgenome data package
BSgenome
Major refactor to the IRanges package. The class system became unwieldy and we decided to make the Sequence virtual class the parent of nearly all classes in this package, much like the vector virtual class is the parent of nearly all classes in the S3 world.
BSgenome
Updates to coincide with changes to AnnotatedList in IRanges.
moved gdApply and related functions from chipseq
BSgenome
Adds simple motif filtering to bsapply.
BSgenome
Fixing man page issue.
Moving file.
Removing man page.
BSgenome
Changes bsapply to take a parameter object BSParams
The existance of a BSParams object should give us better control going
forward for what parameters can be passed into the bsapply function.
The use cases for this function are hightly varied, and so we will
need a way to manage that complexity.
added seed file for BSgenome.Mmusculus.UCSC.mm8
added seed file for BSgenome.Scerevisiae.UCSC.sacCer1
added seed file and tools for BSgenome.Amellifera.BeeBase.assembly4
added subfolder BSgenome.Amellifera.BeeBase.assembly4-tools/ to folder inst/extdata/GentlemanLab/
Unlike for any other UCSC genomes supported so far in Bioconductor, RepeatMasker .out file names for apiMel2 are of the form
Updated incorrect bsapply examples.
added seed file for BSgenome.Amellifera.UCSC.apiMel2
filled the release_name field in BSgenome.Athaliana.TAIR.04232008-seed
added seed file for BSgenome.Athaliana.TAIR.04232008
added seed file for BSgenome.Athaliana.TAIR.01222004
added seed file for BSgenome.Dmelanogaster.UCSC.dm2
added seed file for BSgenome.Rnorvegicus.UCSC.rn4
BSgenome
More documentation.
Documentation for GenomeData and GenomeDataList.
BSgenome
getSeq() now accepts names/start/end/width arguments of arbitrary length (they
are recycled to the longest of them).
Still on the TODO list for getSeq():
(1) return the extracted sequences in a DNAStringSet object;
(2) some speed improvements (takes currently about 35 sec. to extract 1M
short sequences from BSgenome.Mmusculus.UCSC.mm9).
Bummped version to 1.13.5
BSgenome
the single sequences stored in a BSgenome object are now masked by the (inactive) built-in masks at load-time (when built-in masks are included in the BSgenome package for this sequence)
Some improvements to forgeMaskFiles(). Version bumped to 1.9.1
BSgenome
Bumped version to 1.9.23