NEWS

---

GenomicFeatures 1.58.0

NEW FEATURES

• The TxDb class now extends the new OutOfMemoryObject class defined in BiocGenerics (virtual class with no slots).
• Calling saveRDS() on a TxDb object now raises an error with a message that redirects the user to AnnotationDbi::saveDb().

GenomicFeatures 1.56.0

NEW FEATURES

• Add getTerminatorSeq(). Same as getPromoterSeq() but for terminator sequences.

SIGNIFICANT USER-VISIBLE CHANGES

• The makeTxDb*() functions and related have moved to the new txdbmaker package. Full list: - makeTxDb - supportedUCSCtables - browseUCSCtrack - makeTxDbFromUCSC - getChromInfoFromBiomart - makeTxDbFromBiomart - makeTxDbFromEnsembl - makeTxDbFromGRanges - makeTxDbFromGFF - supportedUCSCFeatureDbTracks - supportedUCSCFeatureDbTables - UCSCFeatureDbTableSchema - makeFeatureDbFromUCSC - supportedMiRBaseBuildValues - makePackageName - makeTxDbPackage - makeTxDbPackageFromUCSC - makeFDbPackageFromUCSC - makeTxDbPackageFromBiomart Note that they are still temporarily defined in GenomicFeatures but now they just call the corresponding function in txdbmaker. Since this is a temporary redirect, the user also gets a warning that tells them to use the fully qualified name (e.g. txdbmaker::makeTxDbFromUCSC()) to call the function.

GenomicFeatures 1.54.0

SIGNIFICANT USER-VISIBLE CHANGES

• Fix flaw in heuristic for inferring exon ranks in makeTxDbFromGRanges(): makeTxDbFromGRanges() can guess the exon ranks of a given transcript either (a) based on their position on the chromosome (b) or by looking at the suffixes of the exon ids (e.g. .1, .2, etc...) if any Previously (i.e. in GenomicFeatures < 1.53.1) it was trying (b) first, and would fall back on (a) if (b) failed. Starting with GenomicFeatures 1.53.1, it does the opposite: it tries (a) first, and uses (b) only for exons for which (a) failed. This change addresses the problem that the suffixes of the exon ids cannot be trusted to infer the ranks of exons located on the minus strand. See https://github.com/Bioconductor/GenomicFeatures/issues/59 for an example.
• Try to more clearly distinguish between CDS and CDS parts in documentation.

BUG FIXES

• Switch from HTTP to HTTPS for requests to *.ucsc.edu

GenomicFeatures 1.52.0

NEW FEATURES

• Small improvement to makeTxDbFromEnsembl(): The function can now be called on the abbreviated organism, e.g. "hsapiens", in addition to "homo sapiens".

DEPRECATED AND DEFUNCT

• Finally remove disjointExons() (got deprecated in BioC 3.13 and defunct in BioC 3.15).

BUG FIXES

• Fix issue with order of sequences in seqinfo(makeTxDbFromUCSC()). See commit e4381bc.

GenomicFeatures 1.50.0

SIGNIFICANT USER-VISIBLE CHANGES

• Use useEnsemblGenomes() instead of useMart() wherever possible.
• Improve pcoverageByTranscript() implementation. The function now uses a chunking strategy to handle bigger CompressedGRangesList objects and to reduce memory footprint. Note that even with this improvement, the function is still not very efficient.
• Rename proteinToGenome() argument 'txdb' -> 'db'.

BUG FIXES

• Change test for 'circ_seqs' argument in makeTxDbPackageFromUCSC() from an error to a warning if argument set to NULL.

GenomicFeatures 1.48.0

NEW FEATURES

• Add proteinToGenome() generic and methods. Loosely modeled on ensembldb::proteinToGenome().
• Add extendExonsIntoIntrons().

SIGNIFICANT USER-VISIBLE CHANGES

• Use useEnsembl() instead of useMart() wherever possible.
• makeTxDbFromGFF() and makeTxDbFromGRanges() now recognize and import features of type "gene_segment", "pseudogenic_gene_segment", "antisense_RNA", "three_prime_overlapping_ncrna", or "vault_RNA", as transcripts. Note that, according to the Sequence Ontology, the "gene_segment" and "pseudogenic_gene_segment" terms are NOT offsprings of the "transcript" term via the **is_a** relationship but we still treat them as if they were because that's what Ensembl does in their GFF3 files!

DEPRECATED AND DEFUNCT

• Add warning about FeatureDb-related functionalities no longer being actively maintained.
• disjointExons() is now defunct after being deprecated in BioC 3.13.

GenomicFeatures 1.46.0

SIGNIFICANT USER-VISIBLE CHANGES

• Small update to makeTxDbFromGFF()/makeTxDbFromGRanges(): makeTxDbFromGFF() and makeTxDbFromGRanges() now recognize and import features of type protein_coding_gene (or of type any offspring of the protein_coding_gene term) as genes. This was achieved by adding protein_coding_gene + its offsprings to GenomicFeatures:::.GENE_TYPES.

GenomicFeatures 1.44.0

SIGNIFICANT USER-VISIBLE CHANGES

• Several improvements to makeTxDbFromGFF(): - More GFF3 feature types are recognized as transcripts or genes (commit d7f5980f). - Improve handling of GFF3 files from Ensembl (commit c1e3fb92). - Handle exons with no Parent attribute. GFF3 files that contain exons with no Parent attribute no longer break makeTxDbFromGRanges() or makeTxDbFromGFF(). Orphan exons are dropped.

DEPRECATED AND DEFUNCT

• Deprecate disjointExons() in favor of exonicParts().
• Remove species() method for TxDb objects (was deprecated in BioC 3.3 and defunct in BioC 3.4).

GenomicFeatures 1.42.0

NEW FEATURES

• Implement a restricted seqinfo() setter for TxDb objects that supports altering only the seqlevels and/or genome of the object, but not its seqlengths or circularity flags. This is all we need to make the improved seqlevelsStyle() setter work on TxDb objects (see below).

SIGNIFICANT USER-VISIBLE CHANGES

• The seqlevelsStyle() getter and setter do a better job when the underlying genome is known. See NEWS file in the GenomeInfoDb package for more information.

GenomicFeatures 1.40.0

NEW FEATURES

• Small improvements to makeTxDbFromEnsembl(): - check validity of user supplied transcript attribute code - report nb of fetched transcripts and genes during progress - produced TxDb will "remember" which transcript attribute code was used

SIGNIFICANT USER-VISIBLE CHANGES

• genes() now prints a message when genes are dropped.
• getChromInfoFromUCSC() is now defined in the GenomeInfoDb package. Note that the new function is a much improved version of the old one but also the returned data frame has its columns named differently! See ?getChromInfoFromUCSC in the GenomeInfoDb package for the details.
• Argument 'goldenPath_url' was renamed 'goldenPath.url' in functions makeTxDbFromUCSC(), makeFeatureDbFromUCSC(), makeTxDbPackageFromUCSC(), and makeFDbPackageFromUCSC().
• Default value for argument 'circ_seqs' was changed from DEFAULT_CIRC_SEQS to NULL in all functions that have this argument.
• Global constant DEFAULT_CIRC_SEQS (character vector) was removed. It is now defined in GenomeInfoDb but no longer exported, at least for now.

BUG FIXES

• Make asGFF() method for TxDb objects robust to absence of CDS ranges.

GenomicFeatures 1.38.0

NEW FEATURES

• Small improvement to exonicParts() and intronicParts(): - When 'linked.to.single.gene.only' is set to TRUE, exonicParts() now returns an additional "exonic_part" metadata column that indicates the rank of each exonic part within all the exonic parts linked to the same gene. This is for compatibility with old disjointExons(). - intronicParts() does something similar except that the additional metadata column is named "intronic_part".

SIGNIFICANT USER-VISIBLE CHANGES

• makeTxDbFromGRanges() and makeTxDbFromGFF() now recognize more features as transcripts, exons, or CDS (see commits 822665f8 and 6281f856)

BUG FIXES

• Fix makeTxDbFromUCSC(..., "refGene") for bosTau9/galGal6/panTro6/rheMac10

GenomicFeatures 1.36.0

NEW FEATURES

• Export and document helper functions tidyTranscripts(), tidyExons(), and tidyIntrons()
• Add support for mapToTranscripts() to map ranges that span introns

BUG FIXES

• Fix bug in makeTxDbFromGFF() when file is a GFF3File or GTFFile object
• Fix bug in makeFeatureDbFromUCSC() (see https://github.com/Bioconductor/GenomicFeatures/issues/15)
• Fix makeTxDbFromUCSC() on hg19/refGene and hg38/refGene tables (see message of commit ee575ee8 for more information)

GenomicFeatures 1.34.0

NEW FEATURES

• 2 changes to makeTxDbFromGFF() / makeTxDbFromGRanges(): - Now they support GFF3 files where the CDS parent is an exon instead of a transcript. Note that such GFF3 files are rare and not following the well established convention documented in the GFF3 specs: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md - Now they accept missing/invalid CDS phases (with a warning).
• makeTxDb() now accepts missing CDS phases.

GenomicFeatures 1.32.0

NEW FEATURES

• The first argument of mapToTranscripts() and pmapToTranscripts() now can be a GPos object and a GPos object is returned in that case.
• Add 'use.names' argument to "transcripts", "exons", "cds, and "promoters" methods for TxDb objects.
• makeTxDbFromUCSC() now uses direct SQL queries (to the UCSC MySQL server at genome-mysql.soe.ucsc.edu) instead of rtracklayer::getTable() to fetch data from the Genome Browser. This avoids the issue reported here https://github.com/lawremi/rtracklayer/issues/5 . Another benefit is that direct SQL queries are much faster than rtracklayer::getTable().

SIGNIFICANT USER-VISIBLE CHANGES

• The GRanges object returned by mapToTranscripts() or pmapToTranscripts() takes the transcript lengths as seqlengths.
• pmapToTranscripts() always takes the transcript name as the seqname, even when there is no overlap. Before, it used "UNMAPPED" as the seqname when there was no overlap.

BUG FIXES

• Fix bug where 'coverageByTranscript(x, transcripts)' was erroring in situations where 'transcripts' contains transcripts with an exon that receives no coverage and is located on a sequence for which the seqlength is not available in 'seqinfo(x)' nor in 'seqinfo(transcripts)'.

GenomicFeatures 1.30.0

NEW FEATURES

• Add makeTxDbFromEnsembl() for creating a TxDb object by querying directly an Ensembl MySQL server. This seems to be faster and more reliable than makeTxDbFromBiomart().
• Improve makeTxDbFromBiomart() support for EnsemblGenomes marts fungal_mart, metazoa_mart, plants_mart, and protist_mart.
• makeTxDbFromGFF() and makeTxDbFromGRanges() now import the CDS phase. This required a change in the schema of the underlying SQLite db of TxDb objects. This is still a work-in-progress e.g. cdsBy(txdb, by="tx") still needs to be modified to return the phase info.

SIGNIFICANT USER-VISIBLE CHANGES

• The *ByOverlaps() functions now use the same 'maxgap' and 'minoverlap' defaults as subsetByOverlaps().

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

• exonicParts() and intronicParts() are now documented.
• Address a couple of issues pointed out by Matt Chambers in internal helpers get_organism_from_Ensembl_Mart_dataset() and .extractEnsemblReleaseFromDbVersion() used by makeTxDbFromBiomart().
• Fix internal utility .Ensembl_getMySQLCoreDir(). Was failing for some of the 69 datasets from the Ensembl mart, causing makeTxDbFromBiomart() to fail loopking up the organism scientific name and the chromosome lengths. Thanks to Matt Chambers for reporting this.
• Some tweaks and fixes needed to support RSQLite 2.0.

GenomicFeatures 1.28.0

NEW FEATURES

• makeTxDbFromUCSC() supports new composite "NCBI RefSeq" track for hg38.
• Add 'metadata' argument to makeTxDbFromGFF().
• Add exonicParts() as an alternative to disjointExons(): - exonicParts() has a 'linked.to.single.gene.only' argument (FALSE by default) that is similar to the 'aggregateGenes' argument of disjointExons() but with opposite meaning. More precisely 'exonicParts(txdb, linked.to.single.gene.only=TRUE)' returns the same exonic parts as 'disjointExons(txdb, aggregateGenes=FALSE)'. - Unlike 'disjointExons(txdb, aggregateGenes=TRUE)', 'exonicParts(txdb, linked.to.single.gene.only=FALSE)' does NOT discard exon parts that are not linked to a gene. - exonicParts() is almost twice more efficient than disjointExons().
• Add intronicParts(): similar to exonicParts() but returns intronic parts.

SIGNIFICANT USER-VISIBLE CHANGES

• Some work on distance,GenomicRanges,TxDb method: - pass ignore.strand to range() and distance() - return NA when 'id' cannot be collapsed into a single range or when 'id' is not found in 'y'

DEPRECATED AND DEFUNCT

• Argument 'force' of seqlevels() setters is deprecated in favor of new and more flexible 'pruning.mode' argument.
• Remove the 'vals' argument of the "transcripts", "exons", "cds", and "genes" methods for TxDb objects (was defunct in BioC 3.4).

BUG FIXES

• Fix bug in seqlevels() setter for TxDb objects reported here: https://support.bioconductor.org/p/90226/

GenomicFeatures 1.26.0

NEW FEATURES

• makeTxDbFromGRanges() now recognizes features of type lnc_RNA, antisense_lncRNA, transcript_region, and pseudogenic_tRNA, as transcripts.
• Add 'intronJunctions' argument to mapToTranscripts().

DEPRECATED AND DEFUNCT

• The 'vals' argument of the "transcripts", "exons", "cds", and "genes" methods for TxDb objects is now defunct (was deprecated in BioC 3.3).
• The "species" method for TxDb object is now defunct (was deprecated in BioC 3.3).

GenomicFeatures 1.24.0

NEW FEATURES

• Add mapRangesToIds() and mapIdsToRanges() for mapping genomic ranges to IDs and vice-versa.
• Support makeTxDbFromUCSC("hg38", "knownGene") (gets "GENCODE v22" track).
• Add pmapToTranscripts,GRangesList,GRangesList method.

SIGNIFICANT USER-VISIBLE CHANGES

• Rename the 'vals' argument of the transcripts(), exons(), cds(), and genes() extractors -> 'filter'. The 'vals' argument is still available but deprecated.
• Rename the 'filters' argument of makeTxDbFromBiomart() and makeTxDbPackage() -> 'filter'.
• When grouping the transcripts by exon or CDS, transcriptsBy() now returns a GRangesList object with the "exon_rank" information (as an inner metadata column).
• For transcripts with no exons (like in the GFF3 files from GeneDB), makeTxDbFromGRanges() now infers the exons from the CDS.
• For transcripts with no exons and no CDS (like in the GFF3 files from miRBase), makeTxDbFromGRanges() now infers the exon from the transcript.
• makeTxDbFromGRanges() and makeTxDbFromGFF() now support GFF/GTF files with one (or both) of the following peculiarities: - The file is GTF and contains only lines of type transcript but no transcript_id tag (not clear this is valid GTF but some users are working with this kind of file). - Each transcript in the file is reported to be on its own contig and spans it (start=1) but no strand is reported for the transcript. makeTxDbFromGRanges() now sets the strand to "+" for all these transcripts.
• makeTxDbFromGRanges() now recognizes features of type miRNA, miRNA_primary_transcript, SRP_RNA, RNase_P_RNA, RNase_MRP_RNA, misc_RNA, antisense_RNA, and antisense as transcripts. It also now recognizes features of type transposable_element_gene as genes.
• makeTxDbFromBiomart() now points to the Ensembl mart by default instead of the central mart service.
• Add some commonly used alternative names (Mito, mitochondrion, dmel_mitochondrion_genome, Pltd, ChrC, Pt, chloroplast, Chloro, 2uM) for the mitochondrial and chloroplast genomes to DEFAULT_CIRC_SEQS.

DEPRECATED AND DEFUNCT

• Remove the makeTranscriptDb*() functions (were defunct in BioC 3.2).
• Remove the 'exonRankAttributeName', 'gffGeneIdAttributeName', 'useGenesAsTranscripts', 'gffTxName', and 'species' arguments from the makeTxDbFromGFF() function (were defunct in BioC 3.2).

BUG FIXES

• Try to improve heuristic used in makeTxDbFromGRanges() for detecting the format (GFF3 or GTF) of input GRanges object 'x'.

GenomicFeatures 1.22.0

NEW FEATURES

• Add coverageByTranscript() and pcoverageByTranscript(). See ?coverageByTranscript for more information.
• Various improvements to makeTxDbFromGFF(): - Now supports 'format="auto"' for auto-detection of the file format. - Now supports naming features by dbxref tag (like GeneID). This has proven useful when importing GFFs from NCBI.
• Improvements to the coordinate mapping methods: - Support recycling when length(transcripts) == 1 for parallel mapping functions. - Add pmapToTranscripts,Ranges,GRangesList and pmapFromTranscripts,Ranges,GRangesList methods.
• Adds 'taxonomyId' argument to the makeTxDbFrom*() functions.
• Improvements to makeTxDbPackage(): - Add 'pkgname' argument to makeTxDbPackage() to let the user override the automatic naming of the package to be generated. - Support person objects for 'maintainer' and 'author' arguments to makeTxDbPackage().
• The 'chrominfo' vector passed to makeTxDb() can now mix NAs and non-NAs.

SIGNIFICANT USER-VISIBLE CHANGES

• 2 significant changes to makeTxDbFromGRanges() and makeTxDbFromGFF(): - They now also import transcripts of type pseudogenic_transcript and pseudogenic_exon. - They normally get the "gene_id" and "[tx|exon|CDS]_name" columns from the Name tag. Now they will also infer these columns from the ID tag when the Name tag is missing.
• Improve handling of 'circ_seqs' argument by makeTxDbFromUCSC(), makeTxDbFromGFF(), and makeTxDbFromBiomart(): no more annoying warning when none of the strings in DEFAULT_CIRC_SEQS matches the seqlevels of the TxDb object to be made.
• 2 minor changes to makeTxDbFromBiomart(): - Now drops unneeded chromosome info when importing an incomplete transcript dataset. - Now returns a TxDb object with 'Full dataset' field set to 'no' when makeTxDbFromBiomart() is called with user-supplied 'filters'.
• makeTxDbPackage() now includes data source in the package name by default (for non UCSC and BioMart databases).
• The following changes were made to the coordinate mapping methods: - mapToTranscripts() now reports mapped position with respect to the transcription start site regardless of strand. - Change 'ignore.strand' default from TRUE to FALSE in all coordinate mapping methods for consistency with other functions that already have the 'ignore.strand' argument. - Name matching in mapFromTranscripts() is now done with seqnames(x) and names(transcripts). - The pmapFromTranscripts,*,GRangesList methods now return a GRangesList object. Also they no longer use 'UNMAPPED' seqname for unmapped ranges. - Remove uneeded ellipisis from the argument list of various coordinate mapping methods.
• Change behavior of seqlevels0() getter so it does what it was always intended to do.
• The order of the transcripts returned by transcripts() has changed: now they are guaranteed to be in the same order as in the GRangesList object returned by exonsBy().
• Code improvements and speedup to the transcripts(), exons(), cds(), exonsBy(), and cdsBy() extractors.
• In order to avoid loss of information (and make it reversible with makeTxDbFromGRanges()), the "asGFF" method for TxDb objects now propagates the "exon_name" and "cds_name" columns to the GRanges object.

DEPRECATED AND DEFUNCT

• After being deprecated in BioC 3.1, the makeTranscriptDb*() functions are now defunct.
• After being deprecated in BioC 3.1, the 'exonRankAttributeName', 'gffGeneIdAttributeName', 'useGenesAsTranscripts', 'gffTxName', and 'species' arguments of makeTxDbFromGFF() are now defunct.
• Remove sortExonsByRank() (was defunct in BioC 3.1).

BUG FIXES

• Fix bug in fiveUTRsByTranscript() and threeUTRsByTranscript() extractors when the TxDb object had "user defined" seqlevels and/or a set of "active/inactive" seqlevels defined on it.
• Fix bug in isActiveSeq() setter when the TxDb object had "user defined" seqlevels on it.
• Fix many issues with seqlevels() setter for TxDb objects. In particular make the 'seqlevels(x) <- seqlevels0(x)' idiom work on TxDb objects.
• Fix bug in makeTxDbFromBiomart() when using it to retrieve a dataset that doesn't provide the cds_length attribute (e.g. sitalica_eg_gene dataset in plants_mart_26).

GenomicFeatures 1.20.0

NEW FEATURES

• Add makeTxDbFromGRanges() for extracting gene, transcript, exon, and CDS information from a GRanges object structured as GFF3 or GTF, and returning that information as a TxDb object.
• TxDb objects have a new column ("tx_type" in the "transcripts" table) that the user can request thru the 'columns' arg of the transcripts() extractor. This column is populated when the user makes a TxDb object from Ensembl (using makeTxDbFromBiomart()) or from a GFF3/GTF file (using makeTxDbFromGFF()), but not yet (i.e. it's set to NA) when s/he makes it from a UCSC track (using makeTxDbFromUCSC()). However it seems that UCSC is also providing that information for some tracks so we're planning to have makeTxDbFromUCSC() get it from these tracks in the near future. Also low-level makeTxDb() now imports the "tx_type" column if supplied.
• Add transcriptLengths() for extracting the transcript lengths from a TxDb object. It also returns the CDS and UTR lengths for each transcript if the user requests them.
• extractTranscriptSeqs() now works on a FaFile or GmapGenome object (or, more generally, on any object that supports seqinfo() and getSeq()).

SIGNIFICANT USER-VISIBLE CHANGES

• Renamed makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(), makeTranscriptDbFromGFF(), and makeTranscriptDb() -> makeTxDbFromUCSC(), makeTxDbFromBiomart(), makeTxDbFromGFF(), and makeTxDb(). Old names still work but are deprecated.
• Many changes and improvements to makeTxDbFromGFF(): - Re-implemented it on top of makeTxDbFromGRanges(). - The geneID tag, if present, is now used to assign an external gene id to transcripts that couldn't otherwise be linked to a gene. This is for compatibility with some GFF3 files from FlyBase (see for example dmel-1000-r5.11.filtered.gff included in this package). - Arguments 'exonRankAttributeName', 'gffGeneIdAttributeName', 'useGenesAsTranscripts', and 'gffTxName', are not needed anymore so they are now ignored and deprecated. - Deprecated 'species' arg in favor of new 'organism' arg.
• Some tweaks to makeTxDbFromBiomart(): - Drop transcripts with UTR anomalies with a warning instead of failing. We've started to see these hopeless transcripts with the release 79 of Ensembl in the dmelanogaster_gene_ensembl dataset (based on FlyBase r6.02 / FB2014_05). With this change, the user can still make a TxDb for dmelanogaster_gene_ensembl but some transcripts will be dropped with a warning. - BioMart data anomaly warnings and errors now show the first 3 problematic transcripts instead of 6.
• 'gene_id' metadata column returned by genes() is now a character vector instead of a CharacterList object.
• Use # prefix instead of | in "show" method for TxDb objects.

DEPRECATED AND DEFUNCT

• Deprecated makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(), makeTranscriptDbFromGFF(), and makeTranscriptDb(), in favor of makeTxDbFromUCSC(), makeTxDbFromBiomart(), and makeTxDbFromGFF(), and makeTxDb().
• Deprecated species() accessor in favor of organism() on TxDb objects.
• sortExonsByRank() is now defunct (was deprecated in GenomicFeatures 1.18)
• Removed extractTranscriptsFromGenome(), extractTranscripts(), determineDefaultSeqnameStyle() (were defunct in GenomicFeatures 1.18).

BUG FIXES

• makeTxDbFromBiomart(): - Fix issue causing the download of 'chrominfo' data frame to fail when querying the primary Ensembl mart (with host="ensembl.org" and biomart="ENSEMBL_MART_ENSEMBL"). - Fix issue with error reporting code: when some transcripts failed to pass the sanity checks, the error message was displaying the wrong transcripts. More precisely, many good transcripts were mistakenly added to the set of bad transcripts and included in the error message.
• extractTranscriptSeqs(): fix error message when internal call to exonsBy() fails on 'transcripts'.

GenomicFeatures 1.18.0

NEW FEATURES

• Add extractUpstreamSeqs().
• makeTranscriptDbFromUCSC() now supports the "flyBaseGene" table (FlyBase Genes track).
• makeTranscriptDbFromBiomart() now knows how to fetch the sequence lengths from the Ensembl Plants db.
• makeTranscriptDbFromGFF() is now more tolerant of bad strand information.

SIGNIFICANT USER-VISIBLE CHANGES

• Replace toy TxDb UCSC_knownGene_sample.sqlite (based on hg18) with hg19_knownGene_sample.sqlite (based on hg19) and use hg19 instead of hg18 in all examples (and unit tests).
• Rename TranscriptDb class -> TxDb.
• Now when GTF files are processed into TxDbs with exon ranking being inferreed, if the exons are on separate chromosomes, we toss out that transcript (since we cannot possibly guess the exon ranking correctly).

DEPRECATED AND DEFUNCT

• extractTranscripts() and extractTranscriptsFromGenome() are now defunct.
• Deprecate sortExonsByRank().

BUG FIXES

• Bug fixes and improvements to makeTranscriptDbFromBiomart(): (a) Fix long standing bug where the code in charge of inferring the CDSs from the UTRs would return CDSs spanning all the exons of a non-coding transcript. (b) Fix an issue that was preventing the function from extracting the CDS information added recently to the datasets in the Ensembl Fungi, Ensembl Metazoa, Ensembl Plants, and Ensembl Protists databases. (c) Make the code in charge of extracting the CDSs more robust by taking advantage of new attributes (genomic_coding_start and genomic_coding_end) added by Ensembl in release 74 (Dec 2013), and by adding more sanity checks.

GenomicFeatures 1.14.0

NEW FEATURES

• keys method now has new arguments to allow for more sophisticated filtering.
• adds genes() extractor
• makeTranscriptDbFromGFF() now handles even more different kinds of GFF files.

BUG FIXES

• better argument checking for makeTranscriptDbFromGFF()
• cols arguments and methods will now be columns arguments and methods

GenomicFeatures 1.12.0

NEW FEATURES

• Support for new UCSC species
• Better support for GTF and GFF processing into TranscriptDb objects
• Methods for making TranscriptDb objects from general sources have been made more useful

BUG FIXES

• Updates to allow continued access to ever changing services like UCSC
• Corrections for seqnameStyle methods
• Over 10X performance gains for processing of GTF and GFF files

GenomicFeatures 1.10.0

NEW FEATURES

• Add makeTranscriptDbFromGFF(). Users can now use GFF files to make TranscriptDb resources.
• Add *restricted* "seqinfo<-" method for TranscriptDb objects. It only supports replacement of the sequence names (for now), i.e., except for their sequence names, Seqinfo objects 'value' (supplied) and 'seqinfo(x)' (current) must be identical.
• Add promoters() and getPromoterSeq().
• Add 'reassign.ids' arg (FALSE by default) to makeTranscriptDb().

SIGNIFICANT USER-VISIBLE CHANGES

• Updated vignette.
• Improve how makeTranscriptDbFromUCSC() and makeTranscriptDbFromBiomart() assign internal ids (see commit 65144 for the details).
• 2.5x speedup of fiveUTRsByTranscript() and threeUTRsByTranscript().

DEPRECATED AND DEFUNCT

• Are now defunct: transcripts_deprecated(), exons_deprecated(), and introns_deprecated().
• Deprecate loadFeatures() and saveFeatures() in favor of loadDb() and saveDb(), respectively.

BUG FIXES

• Better handling of BioMart data anomalies.

GenomicFeatures 1.8.0

NEW FEATURES

• Added asBED and asGFF methods to convert a TranscriptDb to a GRanges that describes transcript structures according to either the BED or GFF format. This enables passing a TranscriptDb object to rtracklayer::export directly, when targeting GFF/BED.

GenomicFeatures 1.6.0

NEW FEATURES

• TranscriptDbs are now available as standard packages. Functions that were made available before the last release allow users to create these packages.
• TranscriptDb objects now can be used with select
• select method for TranscriptDb objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package.
• keys now will operate on TranscriptDB objects to expose ID types as potential keys
• keytypes will show which kinds of IDs can be used as a key by select
• cols will display the kinds of data that can be extracted by select
• isActiveSeq has been added to allow entire chromosomes to be toggled active/inactive by the user. By default, everything is exposed, but if you wish you can now easily hide everything that you don't want to see. Subsequence to this, all your accessors will behave as if only the "active" things are present in the database.

SIGNIFICANT USER-VISIBLE CHANGES

• saveDb and loadDb are here and will be replacing saveFeatures and loadFeatures. The reason for the name change is that they dispatch on (and should work with a wider range of object types than just trancriptDb objects (and their associated databases).

BUG FIXES

• ORDER BY clause has been added to SQL statements to enforce more consistent ordering of returned rows.
• bug fixes to enable DB construction to still work even after changes in schemas etc at UCSC, and ensembl sources.
• bug fixes to makeFeatureDbFromUCSC allow it to work more reliably (it was being a little too optimistic about what UCSC would actually supply data for)