CHANGES IN VERSION 1.42.0
-------------------------
BUG FIXES
o Use more robust heuristic in internal helper
get_current_Ensembl_release().
CHANGES IN VERSION 1.40.0
-------------------------
NEW FEATURES
o 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
CHANGES IN VERSION 1.38.0
-------------------------
NEW FEATURES
o 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
o Switch from HTTP to HTTPS for requests to *.ucsc.edu
o Remove library() calls from inst/registered/UCSC_genomes/*.R files
CHANGES IN VERSION 1.36.0
-------------------------
NEW FEATURES
o 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
o Register the following UCSC genomes:
- gorGor6 (linked to Kamilah_GGO_v0)
- xenLae2 (linked to Xenopus_laevis_v2)
o Add Gossypium_hirsutum.txt to inst/extdata/dataFiles/ (provided
by Emory Lucas <bararayung123@hotmail.com>)
o Add 'organism' argument to registered_UCSC_genomes() (contributed by
Kirabo Kakopo).
SIGNIFICANT USER-VISIBLE CHANGES
o UCSC genome hg38 is now based on GRCh38.p14 instead of GRCh38.p13 (this
change originated at UCSC). See commit 091b5d2.
o 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.
o The Accept-organism-for-GenomeInfoDb vignette was converted from
Rnw to Rmd (thanks to Haleema Khan and Jen Wokaty for this conversion).
o Small improvements to low-level helper find_NCBI_assembly_ftp_dir().
CHANGES IN VERSION 1.34.0
-------------------------
NEW FEATURES
o Add update() method for Seqinfo() objects. See '?Seqinfo'.
o Implement getChromInfoFromUCSC() "offline mode" for a selection of
genomes. See '?getChromInfoFromUCSC'.
o 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
o Register the following UCSC genomes: equCab1, equCab2, equCab3,
mpxvRivers, hs1, canFam6, felCat9, xenTro10.
o Export and document find_NCBI_assembly_ftp_dir().
DEPRECATED AND DEFUNCT
o 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.
CHANGES IN VERSION 1.32.0
-------------------------
DEPRECATED AND DEFUNCT
o releaseName() is now defunct on GenomeDescription objects.
o Remove fetchExtendedChromInfoFromUCSC() and available.species().
Both were defunct in BioC 3.14.
CHANGES IN VERSION 1.30.0
-------------------------
NEW FEATURES
o Register NCBI assemblies:
- mRatBN7.2
- UMICH_Zoey_3.1
- Callithrix_jacchus_cj1700_1.1
- MU-UCD_Fhet_4.1 (GCA_011125445.2)
o Register UCSC genomes:
- rn7
- canFam5
- calJac4
SIGNIFICANT USER-VISIBLE CHANGES
o UCSC hg38 genome is now based on GRCh38.p13 instead of GRCh38.p12
o UCSC mm10 genome is now based on GRCm38.p6 instead of GRCm38
o seqlevelsStyle() setter now issues a warning when some seqlevels
cannot be switched.
CHANGES IN VERSION 1.28.0
-------------------------
NEW FEATURES
o 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
o Improve seqinfo<- documentation and error messages.
DEPRECATED AND DEFUNCT
o fetchExtendedChromInfoFromUCSC() is now defunct (was deprecated in
BioC 3.11)
CHANGES IN VERSION 1.26.0
-------------------------
NEW FEATURES
o The seqlevelsStyle() getter and setter now support style "RefSeq" when
the underlying genome is known.
o 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
o 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
o Deprecate releaseName() method for GenomeDescription objects.
BUG FIXES
o Small fix to getChromInfoFromNCBI().
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
-------------------------
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