NEWS

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GenomeInfoDb 1.42.0

BUG FIXES

• Use more robust heuristic in internal helper get_current_Ensembl_release().

GenomeInfoDb 1.40.0

NEW FEATURES

• Register the following NCBI assemblies: - GRCr8 assembly (Rat) - mCavPor4.1 assembly (domestic guinea pig) - 21 Escherichia coli assemblies - a few Petromyzon marinus (sea lamprey) assemblies

GenomeInfoDb 1.38.0

NEW FEATURES

• Register the following NCBI assemblies: - bStrHab1.2.pri (Kakapo) - a few Salmo salar (Atlantic salmon) assemblies - a few African elephant (Loxodonta africana) assemblies

BUG FIXES

• Switch from HTTP to HTTPS for requests to *.ucsc.edu
• Remove library() calls from inst/registered/UCSC_genomes/*.R files

GenomeInfoDb 1.36.0

NEW FEATURES

• Register the following NCBI assemblies: - the bCatUst1.alt.v2 and bCatUst1.pri.v2 assemblies - the felCat9.1_X and F.catus_Fca126_mat1.0 assemblies - the Gossypium_hirsutum_v2.1 assembly - the Kamilah_GGO_v0 assembly - the Xenopus_laevis_v2 and Xenopus_laevis_v10.1 assemblies
• Register the following UCSC genomes: - gorGor6 (linked to Kamilah_GGO_v0) - xenLae2 (linked to Xenopus_laevis_v2)
• Add Gossypium_hirsutum.txt to inst/extdata/dataFiles/ (provided by Emory Lucas <[email protected]>)
• Add 'organism' argument to registered_UCSC_genomes() (contributed by Kirabo Kakopo).

SIGNIFICANT USER-VISIBLE CHANGES

• UCSC genome hg38 is now based on GRCh38.p14 instead of GRCh38.p13 (this change originated at UCSC). See commit 091b5d2.
• The submitters for NCBI assembly Dog10K_Boxer_Tasha have updated the info for the MT sequence, which is reflected in the output of getChromInfoFromNCBI("Dog10K_Boxer_Tasha"). See commit 79a066c.
• The Accept-organism-for-GenomeInfoDb vignette was converted from Rnw to Rmd (thanks to Haleema Khan and Jen Wokaty for this conversion).
• Small improvements to low-level helper find_NCBI_assembly_ftp_dir().

GenomeInfoDb 1.34.0

NEW FEATURES

• Add update() method for Seqinfo() objects. See '?Seqinfo'.
• Implement getChromInfoFromUCSC() "offline mode" for a selection of genomes. See '?getChromInfoFromUCSC'.
• Register the following NCBI assemblies: - a few Triticum aestivum assemblies (bread wheat) - a Pteropus alecto assembly - an Eucalyptus grandis assembly - a few Plasmodium falciparum assemblies (malaria parasite) - the Dog10K_Boxer_Tasha assembly - the Felis_catus_9.0 assembly - the UCB_Xtro_10.0 assembly
• Register the following UCSC genomes: equCab1, equCab2, equCab3, mpxvRivers, hs1, canFam6, felCat9, xenTro10.
• Export and document find_NCBI_assembly_ftp_dir().

DEPRECATED AND DEFUNCT

• Remove releaseName() method for GenomeDescription objects. The releaseName() method for GenomeDescription objects was deprecated in Bioconductor 3.12 and defunct in Bioconductor 3.15. Also move the releaseName() generic function to the BSgenome package.

GenomeInfoDb 1.32.0

DEPRECATED AND DEFUNCT

• releaseName() is now defunct on GenomeDescription objects.
• Remove fetchExtendedChromInfoFromUCSC() and available.species(). Both were defunct in BioC 3.14.

GenomeInfoDb 1.30.0

NEW FEATURES

• Register NCBI assemblies: - mRatBN7.2 - UMICH_Zoey_3.1 - Callithrix_jacchus_cj1700_1.1 - MU-UCD_Fhet_4.1 (GCA_011125445.2)
• Register UCSC genomes: - rn7 - canFam5 - calJac4

SIGNIFICANT USER-VISIBLE CHANGES

• UCSC hg38 genome is now based on GRCh38.p13 instead of GRCh38.p12
• UCSC mm10 genome is now based on GRCm38.p6 instead of GRCm38
• seqlevelsStyle() setter now issues a warning when some seqlevels cannot be switched.

GenomeInfoDb 1.28.0

NEW FEATURES

• Small improvement to the Seqinfo() constructor: if the user doesn't supply the 'seqnames' argument when calling the Seqinfo() constructor, now we try to infer the seqnames from the other arguments.

SIGNIFICANT USER-VISIBLE CHANGES

• Improve seqinfo<- documentation and error messages.

DEPRECATED AND DEFUNCT

• fetchExtendedChromInfoFromUCSC() is now defunct (was deprecated in BioC 3.11)

GenomeInfoDb 1.26.0

NEW FEATURES

• The seqlevelsStyle() getter and setter now support style "RefSeq" when the underlying genome is known.
• Register a bunch of new NCBI assemblies and UCSC genomes. Use registered_NCBI_assemblies() and registered_UCSC_genomes() to get the lists of supported NCBI assemblies and UCSC genomes.

SIGNIFICANT USER-VISIBLE CHANGES

• The seqlevelsStyle() getter and setter do a better job when the underlying genome is known. The new behaviors address two long-standing shortcomings of the old behaviors: - In general, the seqlevelsStyle() setter didn't know how to rename the scaffolds in an object. Now it does. - Also, for some assemblies that use unconventional chromosome naming conventions (e.g. Macaca_fascicularis_5.0), the seqlevelsStyle() getter was not able to detect the naming style and the seqlevelsStyle() setter was not able to rename the chromosomes. Now they both do the right thing. These improvements address these shortcomings but only in the situation where the underlying genome is known e.g. when 'unique(genome(x))' is "macFas5" or "Macaca_fascicularis_5.0". When the underlying genome is not known, nothing has changed.

DEPRECATED AND DEFUNCT

• Deprecate releaseName() method for GenomeDescription objects.

BUG FIXES

• Small fix to getChromInfoFromNCBI().

GenomeInfoDb 1.24.0

NEW FEATURES

• Add getChromInfoFromUCSC(), getChromInfoFromNCBI(), and getChromInfoFromEnsembl().

DEPRECATED AND DEFUNCT

• Deprecate fetchExtendedChromInfoFromUCSC() in favor of getChromInfoFromUCSC().

GenomeInfoDb 1.20.0

SIGNIFICANT USER-VISIBLE CHANGES

• Update genomeMappingTbl.csv, the db used internally by genomeBuilds() and family.

BUG FIXES

• Fix bug in seqlevelsStyle() (see https://github.com/Bioconductor/GenomeInfoDb/issues/3 for more information)
• 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)

GenomeInfoDb 1.18.0

NEW FEATURES

• Add checkCompatibleSeqinfo().

SIGNIFICANT USER-VISIBLE CHANGES

• Update genomeMappingTbl.csv, the db used internally by genomeBuilds() and family.

GenomeInfoDb 1.14.0

DEPRECATED AND DEFUNCT

• 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

• Add missing Y/chrY entry in seqlevel style db for Drosophila melanogaster and Rattus norvegicus.

GenomeInfoDb 1.12.0

NEW FEATURES

• Add function standardChromosomes()
• Seqlevels() setter now supports "fine" and "tidy" modes on GRangesList and GAlignmentsList objects
• Add assembly_accessions dataset

MODIFICATIONS

• Updated mapping table between UCSC and Ensembl to include recent builds
• Use https instead of http to fetch stuff from NCBI
• Replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter
• 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)
• Update files in data directory
• Updated internal functions .lookup_refseq_assembly_accession() and fetch_assembly_report() for speed and efficiency
• move some files from GenomeInfoDb/data/ to GenomeInfoDbData annotation package

BUG FIXES

• fetch_assembly_summary() updated to work with recent changes to format of files assembly_summary_genbank.txt and assembly_summary_refseq.txt

GenomeInfoDb 1.10.0

NEW FEATURES

• Add function mapGenomeBuilds() that maps between UCSC and Ensembl builds.
• Add function genomeBuilds() that list all the available UCSC or Ensembl builds for a given organism[s] that can be used in mapGenomeBuilds()
• Add listOrganism() that list all currently available organism[s] included for use in genomeBuilds()

DEPRECATED AND DEFUNCT

• After being deprecated, the species() method for GenomeDescription objects is now defunct

MODIFICATIONS

• Zebra finch is removed as option for fetchExtendedChromInfoFromUCSC() as it is not support yet
• keepStandardChromosomes() chooses first style when multiple are matched

BUG FIXES

• Fix WARNING occuring when determining style in keepStandardChromosomes()

GenomeInfoDb 0.99.17

MODIFICATIONS

• keepStandardChromosomes: Make 'species' argument optional and remove 'style' argument.

GenomeInfoDb 0.99.14

MODIFICATIONS

• 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<-"

GenomeInfoDb 0.99.7

MODIFICATIONS

• rename: isSupportedSeqnames -> .isSupportedSeqnames supportedSeqnameStyles -> .supportedSeqnameStyles supportedSeqnameMappings -> .supportedSeqnameMappings isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle

GenomeInfoDb 0.99.6

NEW FEATURES

• 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()
• add seqnameStyles generic and method from GenomicRanges

MODIFICATIONS

• rename: testSeqnames -> isSupportedSeqnames
• move SeqnamesStyle generic from GenomicRanges and define a new method which works on a character vector.

DEPRECATED AND DEFUNCT

• deprecate listAllSupportedStylesBySpecies(), listAllSupportedSeqnameStyles(), supportedOrganisms() supportedSeqnameMappingsWithGroup()
• deprecate supportedSeqnameMappings(), supportedSeqnameStyles(), isSupportedSeqnamesStyle(),issupportedSeqnames()

GenomeInfoDb 0.99.1

NEW FEATURES

• added new functions: supportedOrganisms() supportedSeqnameMappingsWithGroup() extractSeqnameSetByGroup()

MODIFICATIONS

• The Seqnames package will have functions which will be moved from AnnotationDbi , GenomicRanges
• List of 9 functions moved from AnnotationDbi supportedSeqnameMappings, findSequenceRenamingMaps, supportedSeqnameStyles, supportedSeqnames, extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle, listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles.
• makeSeqnameIds moved from GenomicRanges
• keepStandardChromosomes moved from GenomicRanges
• rename: keepStandardChromosomes -> keepChromosomes