CHANGES IN VERSION 1.24.0 ------------------------- NEW FEATURES o Add getChromInfoFromUCSC(), getChromInfoFromNCBI(), and getChromInfoFromEnsembl(). DEPRECATED AND DEFUNCT o Deprecate fetchExtendedChromInfoFromUCSC() in favor of getChromInfoFromUCSC(). CHANGES IN VERSION 1.20.0 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Update genomeMappingTbl.csv, the db used internally by genomeBuilds() and family. BUG FIXES o Fix bug in seqlevelsStyle() (see https://github.com/Bioconductor/GenomeInfoDb/issues/3 for more information) o Fix fetchExtendedChromInfoFromUCSC("hg38"), which got broken by a recent change on the UCSC side (see https://support.bioconductor.org/p/117808/#117831 for more information) CHANGES IN VERSION 1.18.0 ------------------------- NEW FEATURES o Add checkCompatibleSeqinfo(). SIGNIFICANT USER-VISIBLE CHANGES o Update genomeMappingTbl.csv, the db used internally by genomeBuilds() and family. CHANGES IN VERSION 1.14.0 ------------------------- NEW FEATURES SIGNIFICANT USER-VISIBLE CHANGES DEPRECATED AND DEFUNCT o Remove 'force' argument from seqinfo() and seqlevels() setters (the argument got deprecated in BioC 3.5 in favor of new and more flexible 'pruning.mode' argument). BUG FIXES o Add missing Y/chrY entry in seqlevel style db for Drosophila melanogaster and Rattus norvegicus. CHANGES IN VERSION 1.12.0 ------------------------- NEW FEATURES o Add function standardChromosomes() o Seqlevels() setter now supports "fine" and "tidy" modes on GRangesList and GAlignmentsList objects o Add assembly_accessions dataset MODIFICATIONS o Updated mapping table between UCSC and Ensembl to include recent builds o Use https instead of http to fetch stuff from NCBI o Replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter o Add 'pruning.mode' argument to the keepSeqlevels(), dropSeqlevels(), and keepStandardChromosomes() functions. IMPORTANT NOTE: Like for the seqlevels() setter, the default pruning mode is "error", which means that now these functions fail when some of the seqlevels to drop from 'x' are in use. The old behavior was to silently prune 'x' (doing "coarse" pruning) o Update files in data directory o Updated internal functions .lookup_refseq_assembly_accession() and fetch_assembly_report() for speed and efficiency o move some files from GenomeInfoDb/data/ to GenomeInfoDbData annotation package BUG FIXES o fetch_assembly_summary() updated to work with recent changes to format of files assembly_summary_genbank.txt and assembly_summary_refseq.txt CHANGES IN VERSION 1.10.0 ------------------------------ NEW FEATURES o Add function mapGenomeBuilds() that maps between UCSC and Ensembl builds. o Add function genomeBuilds() that list all the available UCSC or Ensembl builds for a given organism[s] that can be used in mapGenomeBuilds() o Add listOrganism() that list all currently available organism[s] included for use in genomeBuilds() DEPRECATED AND DEFUNCT o After being deprecated, the species() method for GenomeDescription objects is now defunct MODIFICATIONS o Zebra finch is removed as option for fetchExtendedChromInfoFromUCSC() as it is not support yet o keepStandardChromosomes() chooses first style when multiple are matched BUG FIXES o Fix WARNING occuring when determining style in keepStandardChromosomes() CHANGES IN VERSION 0.99.7 ---------------------------------- MODIFICATIONS o rename: isSupportedSeqnames -> .isSupportedSeqnames supportedSeqnameStyles -> .supportedSeqnameStyles supportedSeqnameMappings -> .supportedSeqnameMappings isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle CHANGES IN VERSION 0.99.6 ---------------------------------- NEW FEATURES o add new functions() seqnamesInGroup which will take a character vector of chromosomes and return the chromosomes specified by the group parameter supplied by the user. The user can also give the species and the style. seqnamesOrder() internally calls Herve's function makeSeqnameIds() o add seqnameStyles generic and method from GenomicRanges MODIFICATIONS o rename: testSeqnames -> isSupportedSeqnames o move SeqnamesStyle generic from GenomicRanges and define a new method which works on a character vector. DEPRECATED AND DEFUNCT o deprecate listAllSupportedStylesBySpecies(), listAllSupportedSeqnameStyles(), supportedOrganisms() supportedSeqnameMappingsWithGroup() o deprecate supportedSeqnameMappings(), supportedSeqnameStyles(), isSupportedSeqnamesStyle(),issupportedSeqnames() CHANGES IN VERSION 0.99.17 ---------------------------------- MODIFICATIONS o keepStandardChromosomes: Make 'species' argument optional and remove 'style' argument. CHANGES IN VERSION 0.99.14 ---------------------------------- MODIFICATIONS o rename: package: Seqnames --> GenomeInfoDb supportedStyles -> genomeStyles makeSeqnameIds --> rankSeqlevels (add to export) seqnamesOrder --> orderSeqlevels extractSeqnameSet -> extractSeqlevels extractSeqnameSetByGroup -> extractSeqlevelsByGroup findSequenceRenamingMaps --> mapSeqlevels seqnamesInGroup --> seqlevelsInGroup seqnamesStyle --> seqlevelsStyle "seqnameStyle<-" --> "seqlevelsStyle<-" CHANGES IN VERSION 0.99.1 ------------------------------ NEW FEATURES o added new functions: supportedOrganisms() supportedSeqnameMappingsWithGroup() extractSeqnameSetByGroup() MODIFICATIONS o The Seqnames package will have functions which will be moved from AnnotationDbi , GenomicRanges o List of 9 functions moved from AnnotationDbi supportedSeqnameMappings, findSequenceRenamingMaps, supportedSeqnameStyles, supportedSeqnames, extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle, listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles. o makeSeqnameIds moved from GenomicRanges o keepStandardChromosomes moved from GenomicRanges o rename: keepStandardChromosomes -> keepChromosomes