Version: 1.64.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The package no longer contains C code. Version: 1.64.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Replace rtracklayer with UCSC.utils in the Suggests field. Version: 1.64.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Use TxDb.Athaliana.BioMart.plantsmart51 instead of TxDb.Athaliana.BioMart.plantsmart22 in vignette. Version: 1.64.0 Category: BUG FIXES Text: Fix small bug in restrict() method for GenomicRanges object. Version: 1.62.0 Category: NEW FEATURES Text: Add makeGPosFromDataFrame(). Version: 1.62.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The package depends on Seqinfo instead of GenomeInfoDb. Version: 1.62.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The package no longer depends on XVector. Version: 1.60.0 Text: No changes in this version. Version: 1.58.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Use hg38 instead of hg19 in vignettes and examples. See commit 57af07f for the details. Version: 1.58.0 Category: BUG FIXES Text: The as.data.frame() methods for GenomicRanges and GPos objects now obey the 'optional' argument. See https://github.com/Bioconductor/GenomicRanges/issues/86 Version: 1.56.0 Category: NEW FEATURES Text: Add terminators() method, same as promoters() but for terminator regions. Version: 1.56.0 Category: BUG FIXES Text: Small fix in makeGRangesFromDataFrame(). Fix error when: (1) input has zero rows, and (2) has no strand field or 'ignore.strand' is TRUE. By Marcel Ramos. See https://github.com/Bioconductor/GenomicRanges/issues/81 Version: 1.54.0 Category: NEW FEATURES Text: Add 'ignore.strand' arg to gaps() method for GenomicRanges objects. Version: 1.54.0 Category: BUG FIXES Text: Small tweaks to GRanges() constructor and to coercion from GPos to GRanges. Version: 1.52.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve documentation of findOverlaps() argument 'minoverlap': The man page now explains how findOverlaps() argument 'minoverlap' is interpreted when 'query' or 'subject' is a GRangesList object. Version: 1.50.0 Text: No changes in this version. Version: 1.48.0 Category: NEW FEATURES Text: Add subtract() for subtracting a set of genomic ranges from a GRanges object. This is similar to bedtools subtract. Version: 1.48.0 Category: NEW FEATURES Text: Add 'na.rm' argument to makeGRangesFromDataFrame(). Version: 1.48.0 Category: DEPRECATED AND DEFUNCT Text: Remove the GenomicRangesList() constructor. This constructor got deprecated in BioC 3.10 and defunct in BioC 3.13. Version: 1.48.0 Category: BUG FIXES Text: Make sure promoters() works on GPos objects. Version: 1.46.0 Text: No changes in this version. Version: 1.44.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Replace KEGG.db usage with KEGGREST in vignettes and examples. Version: 1.44.0 Category: DEPRECATED AND DEFUNCT Text: The GenomicRangesList() constructor is now defunct (got deprecated in BioC 3.10). Version: 1.42.0 Category: NEW FEATURES Text: Add nearestKNeighbors() method for GenomicRanges derivatives. Version: 1.42.0 Category: NEW FEATURES Text: coverage() now supports 'method="naive"'. This is in addition to the already supported methods "sort" and "hash". This new method is a slower version of the "hash" method that has the advantage of avoiding floating point artefacts in the no-coverage regions of the numeric-Rle object returned by coverage() when the weights are supplied as a numeric vector of type 'double'. See "FLOATING POINT ARITHMETIC CAN BRING A SURPRISE" example in '?coverage' in the IRanges package. Version: 1.40.0 Category: NEW FEATURES Text: Add trim() method for GRangesList objects. Version: 1.38.0 Category: NEW FEATURES Text: GPos objects now exist in 2 flavors: UnstitchedGPos and StitchedGPos GPos is now a virtual class with 2 concrete subclasses: UnstitchedGPos and StitchedGPos. In an UnstitchedGPos instance the positions are stored as an integer vector. In a StitchedGPos instance, like with old GPos instances, the positions are stored as an IRanges object where each range represents a run of consecutive positions. This is analog to the IPos/UnstitchedIPos/StitchedIPos situation. See ?GPos for more information. Old serialized GPos instances can be converted to StitchedGPos instances with updateObject(). Version: 1.38.0 Category: NEW FEATURES Text: GPos objects now can hold names Version: 1.38.0 Category: NEW FEATURES Text: Coercion to GPos now propagates the names Version: 1.38.0 Category: NEW FEATURES Text: Add GRangesFactor class (Factor derivative). See ?GRangesFactor Version: 1.38.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Export from_GPos_to_GRanges() Version: 1.38.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Some reorgnization of the GenomicRangesList hierarchy (see commit f988a5a9). Version: 1.38.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Swap order of arguments 'seqlengths' and 'seqinfo' of the GRanges() constructor so now the latter comes before the former. Version: 1.38.0 Category: DEPRECATED AND DEFUNCT Text: Remove findOverlaps, seqnames, and seqinfo<- methods for RangedData objects. These methods were deprecated in BioC 3.8 and defunct in BioC 3.9. Version: 1.38.0 Category: BUG FIXES Text: Coercion from RangesList to GRanges is more robust to seqlevel differences Version: 1.38.0 Category: BUG FIXES Text: Fix bug in isSmallGenome() (introduced by change in sum() in R >= 3.5) Version: 1.36.0 Category: NEW FEATURES Text: findOverlaps() now supports type="equal" on GRangesList objects Version: 1.36.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.8, the seqinfo() setter, seqnames(), and findOverlaps() are now defunct on RangedData objects. Version: 1.34.0 Category: NEW FEATURES Text: Add coercions from GenomicRanges to IRangesList and from GenomicRanges to CompressedIRangesList. These 2 new coercions are equivalent to coercion from GenomicRanges to IntegerRangesList, that is, if 'gr' is a GenomicRanges object, the 3 following coercions are equivalent and return the same CompressedIRangesList object: as(gr, "IntegerRangesList") as(gr, "IRangesList") as(gr, "CompressedIRangesList") Version: 1.34.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate several RangedData methods: seqinfo, seqinfo<-, seqnames, and findOverlaps#RangedData#GenomicRanges RangedData objects will be deprecated in BioC 3.9 (their use has been discouraged since BioC 2.12, that is, since 2014). Package developers that are still using RangedData objects need to migrate their code to use GRanges or GRangesList objects instead. Version: 1.34.0 Category: BUG FIXES Text: Make [[, as.list(), lapply(), and unlist() fail more graciously on a GenomicRanges object. Version: 1.34.0 Category: BUG FIXES Text: Make "show" methods for GenomicRanges and GPos objects robust to special metadata column names like "stringsAsFactors". Version: 1.34.0 Category: BUG FIXES Text: Export the "update" method for GRanges objects. This addresses https://github.com/Bioconductor/GenomicRanges/issues/7 Version: 1.32.0 Category: NEW FEATURES Text: 2 improvements to the "promoters" method for GenomicRanges objects: - The 'upstream' and 'downstream' arguments now can be integer vectors parallel to 'x', - The 'use.names' argument now is supported. This is for consistency with the other intra range transformations. Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GenomicRanges now is a List subclass. This means that GRanges objects and their derivatives are now considered list-like objects (even though [[ don't work on them yet, this will be implemented in Bioconductor 3.8). Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add the CompressedGRangesList class as a replacement for the GRangesList class. The long term goal is that GRangesList becomes a virtual class with CompressedGRangesList as a concrete subclass. Note that the GRangesList() constructor now returns a CompressedGRangesList instance instead of a GRangesList instance. Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GenomicRangesList is now a virtual class (like IntegerRangesList is). Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GRanges derivatives no longer support the 'x[i, j] <- value' form of subassignment. This feature was of very limited usefulness and no Bioconductor package was using it. Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve performance of nearest(), precede(), and follow() on a GRanges object. Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve performance of coverage() on a GPos object. Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve performance of sort() on a GRangesList object. Also now it supports 'ignore.strand'. See https://github.com/Bioconductor/GenomicRanges/issues/1 (and note how unnicely these changes were requested). Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve performance and error handling of coercion from RleList to GRanges. This is a 50x speedup or more when the RleList object to coerce has thousands of list elements or more. Version: 1.32.0 Category: BUG FIXES Text: Fix coercion from RleList to GRanges when some list elements in the object to coerce have length 0 (see https://support.bioconductor.org/p/105926/ for original report by Xiaotong Yao). Version: 1.32.0 Category: BUG FIXES Text: Fix bug in nearest() when an unstranded range in 'query' precedes or follows more than one range in 'subject'. Version: 1.30.0 Category: NEW FEATURES Text: Support GPos-based GRangesList objects. Version: 1.30.0 Category: NEW FEATURES Text: Add 'na.rm' argument to binnedAverage(). Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change 'maxgap' and 'minoverlap' defaults for findOverlaps() and family (i.e. countOverlaps(), overlapsAny(), and subsetByOverlaps()). This change addresses 2 long-standing issues: (1) by default zero-width ranges are not excluded anymore, and (2) control of zero-width ranges and adjacent ranges is finally decoupled (only partially though). New default for 'minoverlap' is 0 instead of 1. New default for 'maxgap' is -1 instead of 0. See ?findOverlaps for more information about 'maxgap' and the meaning of -1. For example, if 'type' is "any", you need to set 'maxgap' to 0 if you want adjacent ranges to be considered as overlapping. Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GPos now extends GRanges but with a ranges slot that must be an IPos object. Update "old" GPos objects with updateObject(). Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move pos() generic to IRanges package. Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move rglist() generic to IRanges package. Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Rename GenomicRangesORmissing and GenomicRangesORGRangesList classes -> GenomicRanges_OR_missing and GenomicRanges_OR_GRangesList, respectively. Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove "seqinfo" method for RangesList objects. Version: 1.30.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove "stack" method for GenomicRangesList objects. Version: 1.30.0 Category: DEPRECATED AND DEFUNCT Text: 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). Version: 1.30.0 Category: BUG FIXES Text: nearest() and distanceToNearest() now call findOverlaps() internally with maxgap=0 and minoverlap=0. This fixes incorrect results obtained in some situations e.g. in the situation reported here: https://support.bioconductor.org/p/99369/ (zero-width ranges) but also in this situation: nearest(GRanges("chr1", IRanges(5, 10)), GRanges("chr1", IRanges(1, 4:5)), select="all") where the 2 ranges in the subject are *both* nearest to the 5-10 range. Version: 1.30.0 Category: BUG FIXES Text: '$' completion on GenomicRanges works in RStudio. Version: 1.30.0 Category: BUG FIXES Text: Minor tweaks to conversion from character to GRanges and reverse conversion. Version: 1.28.0 Category: NEW FEATURES Text: Add coercion from ordinary list to GRangesList. Also the GRangesList() constructor function now accepts a list of GRanges as input (and just calls new coercion from list to GRangesList on it internally). Version: 1.28.0 Category: NEW FEATURES Text: seqlevels() setter now supports "fine" and "tidy" pruning modes on GRangesList objects (in addition to "coarse" mode, which is the default). Version: 1.28.0 Category: NEW FEATURES Text: "range" methods now have a 'with.revmap' argument (like "reduce" and "disjoin" methods). Version: 1.28.0 Category: NEW FEATURES Text: Add a bunch of range-oriented methods for GenomicRangesList objects. Version: 1.28.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Some changes/improvements to "precede" and "follow" methods for GenomicRanges objects motivated by discussion on support site: https://support.bioconductor.org/p/90664/ Version: 1.28.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Some changes/improvements to "rank" method for GenomicRanges objects: - now supports the same ties methods as base::rank() (was only supporting ties methods "first" and "min" until now) - default ties method now is "average", like base::rank() - now supports additional argument 'ignore.strand'. Version: 1.28.0 Category: DEPRECATED AND DEFUNCT Text: Argument 'force' of seqinfo() and seqlevels() setters is deprecated in favor of new and more flexible 'pruning.mode' argument. Version: 1.28.0 Category: BUG FIXES Text: Fix severe performance regression introduced in Bioconductor 3.3 in "intersect" and "setdiff" methods for GRangesList objects. Thanks to Jens Reeder for catching and reporting this. Version: 1.26.0 Category: NEW FEATURES Text: Add 'with.revmap' argument to "reduce" method for GRangesList objects. Version: 1.26.0 Category: NEW FEATURES Text: Add 'with.revmap' argument to various "disjoin" methods. Version: 1.26.0 Category: NEW FEATURES Text: makeGRangesFromDataFrame() now tries to turn the "start" and "end" columns of the input data frame into numeric vectors if they are not already. Version: 1.26.0 Category: NEW FEATURES Text: Add makeGRangesListFromDataFrame() function. Version: 1.26.0 Category: NEW FEATURES Text: Add "summary" method for GenomicRanges objects. Version: 1.26.0 Category: NEW FEATURES Text: Add 'use.names' argument to the granges(), grglist(), and rglist() generics and methods, as well as to a bunch of "ranges" methods (for GRanges, GPos, GNCList, GRangesList, and DelegatingGenomicRanges). Default is TRUE to preserve existing behavior. Version: 1.26.0 Category: NEW FEATURES Text: Add 'use.mcols' arguments to the "ranges" methods for GPos objects. Version: 1.26.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Version: 1.26.0 Category: DEPRECATED AND DEFUNCT Text: Version: 1.26.0 Category: BUG FIXES Text: Fix bug in distanceToNearest() related to ranges starting at zero. Version: 1.26.0 Category: BUG FIXES Text: Fix GRanges(Seqinfo()). Version: 1.24.0 Category: NEW FEATURES Text: Add the GPos class, a container for storing a set of "genomic positions" (i.e. genomic ranges of width 1). Even though a GRanges object can be used for that, using a GPos object can be much more memory-efficient, especially when the object contains long runs of adjacent positions. Version: 1.24.0 Category: NEW FEATURES Text: Add a bunch of "invertStrand" methods to support strand inversion of any "stranded" object (i.e. any object with a strand() getter and setter). E.g. invertStrand() works on GRanges, GRangesList, GAlignments, GAlignmentPairs, GAlignmentsList, and RangedSummarizedExperiment objects. Version: 1.24.0 Category: NEW FEATURES Text: Add "is.unsorted" method for GenomicRanges objects (contributed by Pete Hickey). Version: 1.24.0 Category: NEW FEATURES Text: base::rank() gained a new 'ties.method="last"' option and base::order() a new argument ('method') in R 3.3. Thus so do the "rank" and "order" methods for GenomicRanges objects. Version: 1.24.0 Category: NEW FEATURES Text: Add "selfmatch" method for GenomicRanges objects. Version: 1.24.0 Category: NEW FEATURES Text: Add "union" method for GRangesList objects. Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove old SummarizedExperiment class from the GenomicRanges package (this class is now defined in the SummarizedExperiment package). Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move the following generic functions from the GenomicRanges package to the SummarizedExperiment package: - SummarizedExperiment - exptData, "exptData<-" - rowRanges, "rowRanges<-" - colData, "colData<-" - assayNames, "assayNames<-" - assays, "assays<-" - assay, "assay<-" Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Rename "pintersect" and "psetdiff" methods for GRangesList objects -> "intersect" and "setdiff" without changing their behavior (they still do mendoapply(intersect, x, y) and mendoapply(setdiff, x, y), respectively). The old names were misnomers (see svn commit message for commit 113793 for more information). Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove the ellipsis (...) from all the setops methods, except from: - "punion" method for signature GRanges#GRangesList; - "pintersect" and "psetdiff" methods for signature GRangesList#GRangesList; - "pgap" method for GRanges objects. Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Use DESeq2 instead of DESeq in the vignettes (better late than never). Version: 1.24.0 Category: DEPRECATED AND DEFUNCT Text: Remove GIntervalTree class and methods (were defunct in BioC 3.2). Version: 1.24.0 Category: DEPRECATED AND DEFUNCT Text: Remove mapCoords() and pmapCoords() (were defunct in BioC 3.2). Version: 1.22.0 Category: NEW FEATURES Text: Support coercions back and forth between a GRanges object and a character vector (or factor) with elements in the format 'chr1:2501-2800' or 'chr1:2501-2800:+'. Version: 1.22.0 Category: NEW FEATURES Text: Add facilities for manipulating "genomic variables": bindAsGRanges(), mcolAsRleList(), and binnedAverage(). See ?genomicvars for more information. Version: 1.22.0 Category: NEW FEATURES Text: Add "narrow" method for GRangesList objects. Version: 1.22.0 Category: NEW FEATURES Text: Enhancement to the GRanges() constructor. If the 'ranges' argument is not supplied then the constructor proceeds in 2 steps: 1. An initial GRanges object is created with 'as(seqnames, "GRanges")'. 2. Then this GRanges object is updated according to whatever other arguments were supplied to the call to GRanges(). Because of this enhancement, GRanges(x) is now equivalent to 'as(x, "GRanges")' e.g. GRanges() can be called directly on a character vector representing ranges, or on a data.frame, or on any object for which coercion to GRanges is supported. Version: 1.22.0 Category: NEW FEATURES Text: Add 'ignore.strand' argument to "range" and "reduce" methods for GRangesList objects. Version: 1.22.0 Category: NEW FEATURES Text: Add coercion from SummarizedExperiment to RangedSummarizedExperiment (also available via updateObject()). See 1st item in DEPRECATED AND DEFUNCT section below for more information about this. Version: 1.22.0 Category: NEW FEATURES Text: GNCList objects are now subsettable. Version: 1.22.0 Category: NEW FEATURES Text: "coverage" methods now accept 'shift' and 'weight' supplied as an Rle. Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Modify behavior of "*" strand in precede() / follow() to mimic 'ignore.strand=TRUE'. Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Revisit "pintersect" methods for GRanges#GRanges, GRangesList#GRanges, and GRanges#GRangesList: - Sanitize their semantic. - Add 'drop.nohit.ranges' argument (FALSE by default). - If 'drop.nohit.ranges' is FALSE, the returned object now has a "hit" metadata column added to it to indicate the elements in 'x' that intersect with the corresponding element in 'y'. Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: binnedAverage() now treats 'numvar' as if it was set to zero on genomic positions where it's not set (typically happens when 'numvar' doesn't span the entire chromosomes because it's missing the trailing zeros). Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GRanges() constructor no more mangles the names of the supplied metadata columns (e.g. if the column is "_tx_id"). Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: makeGRangesFromDataFrame() now accepts "." in strand column (treated as Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GNCList() constructor now propagates the metadata columns. Version: 1.22.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove "seqnames" method for RangesList objects. Version: 1.22.0 Category: DEPRECATED AND DEFUNCT Text: The SummarizedExperiment class defined in GenomicRanges is deprecated and replaced by 2 new classes defined in the new SummarizedExperiment package: SummarizedExperiment0 and RangedSummarizedExperiment. In BioC 2.3, the SummarizedExperiment class will be removed from the GenomicRanges package and the SummarizedExperiment0 class will be renamed SummarizedExperiment. To facilitate this transition, a coercion method was added to coerce from old SummarizedExperiment to new RangedSummarizedExperiment (this coercion is performed when calling updateObject() on an old SummarizedExperiment object). Version: 1.22.0 Category: DEPRECATED AND DEFUNCT Text: makeSummarizedExperimentFromExpressionSet() and related stuff was moved to the new SummarizedExperiment package. Version: 1.22.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.1, the rowData accessor is now defunct (replaced with the rowRanges accessor). Version: 1.22.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.1, GIntervalTree objects and the "intervaltree" algorithm in findOverlaps() are now defunct. Version: 1.22.0 Category: DEPRECATED AND DEFUNCT Text: After being deprecated in BioC 3.1, mapCoords() and pmapCoords() are now defunct. Version: 1.22.0 Category: BUG FIXES Text: 2 tweaks to subsetting *by* an GenomicRanges: - Improve speed when the object to subset is a SimpleList (e.g. SimpleRleList). - Fix issue when the GenomicRanges subscript is empty. Version: 1.20.0 Category: NEW FEATURES Text: Add coercion methods to go back and forth between ExpressionSet and SummarizedExperiment. Version: 1.20.0 Category: NEW FEATURES Text: Add 'assayNames', 'assayNames<-' for SummarizedExperiment Version: 1.20.0 Category: NEW FEATURES Text: assays() supports arrays of up to 4 dimensions. Version: 1.20.0 Category: NEW FEATURES Text: Add GNCList() for preprocessing a GenomicRanges object into a GNCList object that can be used for fast overlap seach with findOverlaps(). GNCList() is a replacement for GIntervalTree() that uses Nested Containment Lists instead of interval trees. Unlike GIntervalTree(), GNCList() supports preprocessing of a GenomicRanges object with ranges located on a circular sequence. For a one time use, it's not advised to explicitely preprocess the input. This is because findOverlaps() or countOverlaps() will take care of it and do a better job at it (that is, they preprocess only what's needed when it's needed and release memory as they go). Version: 1.20.0 Category: NEW FEATURES Text: All "findOverlaps" methods now support 'select' equal "last" or "arbitrary" (in addition to "all" and "first"). Version: 1.20.0 Category: NEW FEATURES Text: Add absoluteRanges() and relativeRanges() to transform back and forth between absolute and relative genomic ranges. Version: 1.20.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Renamed 'rowData' and 'rowData<-' -> 'rowRanges', 'rowRanges<-'. Old names still work but are deprecated. Version: 1.20.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Some improvements to makeGRangesFromDataFrame(): - Improve internal logic used for finding the GRanges columns in the input. - If 'seqinfo' is not supplied, the seqlevels are now ordered according to the output of GenomeInfoDb::rankSeqlevels(). - Now an attempt is made to turn 'df' into a data frame (with 'as.data.frame(df)') if it's not a data frame or a DataFrame object. Version: 1.20.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The GRanges() constructor now propagates the metadata cols that are on 'ranges' if no metadata cols are explicitly passed to the constructor. Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated 'rowData' and 'rowData<-' in favor of 'rowRanges' and 'rowRanges<-'. Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated mapCoords() and pmapCoords(). They're replaced by mapToTranscripts() and pmapToTranscripts() from the GenomicFeatures package and mapToAlignments() and pmapToAlignments() from the GenomicAlignments package. Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated GIntervalTree objects. Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Removed "map" and "splitAsListReturnedClass" methods (were defunct in GenomicRanges 1.18.0). Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Removed makeSeqnameIds() (was defunct in GenomicRanges 1.18.0). Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Removed 'with.mapping' argunment from "reduce" methods (was defunct in GenomicRanges 1.18.0). Version: 1.20.0 Category: BUG FIXES Text: Fix 'findOverlaps(..., type="start")' on GRangesList objects which has been broken for years. Version: 1.20.0 Category: BUG FIXES Text: Fix self overlap search on a GRanges object when 'ignore.strand=TRUE' (i.e. 'findOverlaps(gr, ignore.strand=TRUE)'). Version: 1.18.0 Category: NEW FEATURES Text: Add 'use.mcols' arg to "ranges" method for GRangesList objects. Version: 1.18.0 Category: NEW FEATURES Text: "assays<-" methods may be invoked with 'withDimnames' arg. Version: 1.18.0 Category: NEW FEATURES Text: Add mapCoords() generic and methods (replacing map()). Version: 1.18.0 Category: NEW FEATURES Text: Add granges,GenomicRanges method. Version: 1.18.0 Category: NEW FEATURES Text: Add strand<-,GRangesList,character method for global replacement (i.e., all strands become 'value'). Version: 1.18.0 Category: NEW FEATURES Text: Add resize,GRangesList-method. Version: 1.18.0 Category: NEW FEATURES Text: Add DelegatingGenomicRanges class and vignette on how to extend GenomicRanges. Version: 1.18.0 Category: NEW FEATURES Text: Document subsetting a named list-like object by a GRanges subscript. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Modify "show" methods for GRanges and GRangesList objects so they print a 1-line summary of the seqinfo component. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove as.data.frame,GRangesList-method; use as.data.frame,List. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: "trim" method for GenomicRanges only trims out-of-bound ranges on non-circular sequences whose length is not NA. This behavior is consistent with the GenomicRanges validity method. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Changes to flank(), resize() and start/end/width setters: - no longer trim the result ranges when called on a GRanges - warning is issued by GenomicRanges validity method when out-of-bound ranges are on non-circular sequences whose length is not NA Note this behavior is now consistent with that of shift(). Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up validation of GenomicRanges objects by 1.2x. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up trim() on GenomicRanges objects by 1.2x. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improve warning when GenomicRanges object contains out-of-bound ranges. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Work on vignette HOWTOs: - split 'How to read BAM files into R' into 3 HOWTOs - split 'How to prepare a table of read counts for RNA-Seq differential gene expression' into 3 HOWTOs - split 'How to extract DNA sequences of gene regions' into 2 HOWTOs - make individual HOWTOs subsections of single HOWTO section Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Follow renaming of TranscriptDb class to TxDb. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Replace references to plantsmart21 with plantsmart22. Version: 1.18.0 Category: DEPRECATED AND DEFUNCT Text: Defunct map() (skip deprecation). Replace with mapCoords(). Version: 1.18.0 Category: BUG FIXES Text: [cr]bind,SummarizedExperiment methods respect derived classes. Version: 1.18.0 Category: BUG FIXES Text: assays(se, withDimnames=TRUE) <- value no longer tries to access a slot 'withDimnames'. Version: 1.18.0 Category: BUG FIXES Text: cbind and rbind,SummarizedExperiment-methods respect derived classes Version: 1.18.0 Category: BUG FIXES Text: "ranges" method for GRangesList objects should not propagate inner metadata columns by default. Version: 1.18.0 Category: BUG FIXES Text: GRanges() constructor now preserves the seqlevels in the order supplied by the user. Version: 1.18.0 Category: BUG FIXES Text: Ensure tileGenome() breakpoints do not extend past end of genome. Version: 1.18.0 Category: BUG FIXES Text: Fix "show" method for GenomicRanges objects when 'showHeadLines' global option is set to Inf. Version: 1.18.0 Category: BUG FIXES Text: [rc]bind,SummarizeExperiment-methods now compare all elements. Version: 1.18.0 Category: BUG FIXES Text: Remove "==" and "<=" methods for GenomicRanges objects (not needed). Version: 1.16.0 Category: NEW FEATURES Text: Add "subset" method for SummarizedExperiment objects. Version: 1.16.0 Category: NEW FEATURES Text: Allow DataFrame in SummarizedExperiment assays. Version: 1.16.0 Category: NEW FEATURES Text: Add 'use.mcols' arg (FALSE by default) to the granges(), grglist(), and rglist() generics (a.k.a. the range-squeezer generics). Version: 1.16.0 Category: NEW FEATURES Text: Add coercion method from GRangesList to RangesList. Version: 1.16.0 Category: NEW FEATURES Text: Add score() setter for GRangesList objects. Version: 1.16.0 Category: NEW FEATURES Text: findOverlaps(..., type="within") now works on circular chromosomes. Version: 1.16.0 Category: NEW FEATURES Text: Add 'ignore.strand' arg to "sort" method for GRanges objects. Version: 1.16.0 Category: NEW FEATURES Text: Support subsetting of a named list-like object *by* a GenomicRanges subscript. Version: 1.16.0 Category: NEW FEATURES Text: Support sort(granges, by = ~ score), i.e., a formula-based interface for sorting by the mcols. Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move many functionalities to the new GenomicAlignments package: - The GAlignments, GAlignmentPairs, and GAlignmentsList classes. - The qnarrow() generic and methods. - The "narrow" and "pintersect" methods for GAlignments and GAlignmentsList objects. - The low-level CIGAR utilities. - The "findOverlaps" methods for GAlignment* objects. - The summarizeOverlaps() generic and methods, and the "Counting reads with summarizeOverlaps" vignette. - findCompatibleOverlaps() and countCompatibleOverlaps(). - The findSpliceOverlaps() generic and methods. - The "overlap encodings" stuff i.e. the "encodeOverlaps" method for GRangesList objects, flipQuery(), selectEncodingWithCompatibleStrand(), isCompatibleWithSplicing(), isCompatibleWithSkippedExons(), extractSteppedExonRanks(), extractSpannedExonRanks(), extractSkippedExonRanks(), and extractQueryStartInTranscript(), and the "OverlapEncodings" vignette. Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Rename 'with.mapping' arg -> 'with.revmap' in "reduce" methods. The old arg name is still working but deprecated. Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move makeSeqnameIds() function to the new GenomeInfoDb package and rename it rankSeqlevels(). The old name is still working but deprecated. Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The "strand" methods now perform stricter checking and are guaranteed to always return a factor (or factor-Rle) with the "standard strand levels" and no NAs. Or to fail. Version: 1.16.0 Category: BUG FIXES Text: Tweaks and fixes to various "strand" methods: - Methods for character vectors and factors do not accept NAs anymore (they raise an error). - Methods for integer and logical vectors map NAs to * (instead of NA). - Method for Rle objects now also works on character-, factor-, and integer-Rle objects (in addition to logical-Rle objects). Version: 1.14.0 Category: NEW FEATURES Text: Add coercion from GenomicRangesList to RangedDataList. Version: 1.14.0 Category: NEW FEATURES Text: Add "c" method for GAlignmentPairs objects. Version: 1.14.0 Category: NEW FEATURES Text: Add coercion from GAlignmentPairs to GAlignmentsList. Version: 1.14.0 Category: NEW FEATURES Text: Add 'inter.feature' and 'fragment' arguments to summarizeOverlaps(). Version: 1.14.0 Category: NEW FEATURES Text: Add seqselect,GAlignments-method. Version: 1.14.0 Category: NEW FEATURES Text: Add CIGAR utilities: explodeCigarOps(), explodeCigarOpLengths() cigarRangesAlongReferenceSpace(), cigarRangesAlongQuerySpace() cigarRangesAlongPairwiseSpace(), extractAlignmentRangesOnReference() cigarWidthAlongReferenceSpace(), cigarWidthAlongQuerySpace() cigarWidthAlongPairwiseSpace(). Version: 1.14.0 Category: NEW FEATURES Text: Add seqlevels0() and restoreSeqlevels(). Version: 1.14.0 Category: NEW FEATURES Text: Add seqlevelsInUse() getter for GRanges, GRangesList, GAlignments GAlignmentPairs, GAlignmentsList and SummarizedExperiment objects. Version: 1.14.0 Category: NEW FEATURES Text: Add update,GAlignments method. Version: 1.14.0 Category: NEW FEATURES Text: Add GIntervalTree class. Version: 1.14.0 Category: NEW FEATURES Text: Add coercion from GAlignmentPairs to GAlignments. Version: 1.14.0 Category: NEW FEATURES Text: Add sortSeqlevels(). Version: 1.14.0 Category: NEW FEATURES Text: Add tileGenome(). Version: 1.14.0 Category: NEW FEATURES Text: Add makeGRangesFromDataFrame() and coercion from data.frame or DataFrame to GRanges. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Renaming (with aliases from old to new names): - classes GappedAlignments -> GAlignments GappedAlignmentPairs -> GAlignmentPairs - functions GappedAlignments() -> GAlignments() GappedAlignmentPairs() -> GAlignmentPairs() readGappedAlignments() -> readGAlignments() readGappedAlignmentPairs() -> readGAlignmentPairs() Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove 'asProperPairs' argument to readGAlignmentsList(). Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Modify "show" method for Seqinfo object to honor showHeadLines and showTailLines global options. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 50x speedup or more when merging 2 Seqinfo objects, 1 very small and 1 very big. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add dependency on new XVector package. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Enhanced examples for renaming seqlevels in seqlevels-utils.Rd. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: More efficient reference class constructor for 'assays' slot of SummarizedExperiment objects. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 'colData' slot of SummarizedExperiment produced from call to summarizedOverlaps() now holds the class type and length of 'reads'. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 4x speedup to cigarToRleList(). Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Relax SummarizedExperiment class validity. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Renaming (with aliases from old to new names): cigarToWidth() -> cigarWidthOnReferenceSpace(), and cigarToQWidth() -> cigarWidthOnQuerySpace(). Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improvements to summarizeOverlaps(): - mode 'Union': 1.5x to 2x speedup - mode 'IntersectionNotEmpty': 2x to 8x speedup + memory footprint reduced by ~ half Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change default 'use.names' to FALSE for readGAlignmentsList(). Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Implement 'type="equal"' for findOverlaps,SummarizedExperiment methods. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Modify summarizeOverlaps() examples to use 'asMates=TRUE' instead of 'obeyQname=TRUE'. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove unneeded "window" method for GenomicRanges objects. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up seqinfo() getter and setter on SummarizedExperiment objects and derivatives (e.g. VCF) by using direct access to 'rowData' slot. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: coverage,GenomicRanges method now uses .Ranges.coverage() when using the defaults for 'shift' and 'width'. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove restriction that metadata column names must be different on a GRangesList and the unlisted GRanges. Version: 1.14.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: GenomicRangesUseCases vignette has been redone and renamed to GenomicRangesHOWTOs. Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: Defunct all "match" and "%in%" methods in the package except for those with the GenomicRanges,GenomicRanges signature. Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate GappedAlignment*: - GappedAlignments and GappedAlignmentPairs classes - GappedAlignments() and GappedAlignmentPairs() constructors - readGappedAlignments() and readGappedAlignmentPairs() functions Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate cigar util functions: cigarToWidth(), cigarToQWidth(), cigarToIRanges() splitCigar(), cigarToIRanges(), cigarToIRangesListByAlignment() cigarToIRangesListByRName(), cigarToWidth(), cigarToQWidth() cigarToCigarTable(), summarizeCigarTable() Version: 1.14.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate seqselect(). Version: 1.14.0 Category: BUG FIXES Text: Fix bug in c,GAlignments for case when objects were unnamed. Version: 1.14.0 Category: BUG FIXES Text: Fix bug in flank,GenomicRanges (when 'ignore.strand=TRUE' 'start' was being set to TRUE). Version: 1.14.0 Category: BUG FIXES Text: Fix bug in behavior of summarizeOverlaps() count mode 'IntersectionNotEmpty' when 'inter.features=FALSE'. Shared regions are now removed before counting. Version: 1.14.0 Category: BUG FIXES Text: Fix bug in cigarToIRangesListByAlignment() when 'flag' is supplied and indicates some reads are unmapped. Version: 1.14.0 Category: BUG FIXES Text: Fix bug in summarizeOverlaps(..., mode='IntersectionNotEmpty') when 'features' has '-' and '+' elements and 'ignore.strand=TRUE'. Version: 1.14.0 Category: BUG FIXES Text: match,GenomicRanges,GenomicRanges method now handles properly objects with seqlevels not in the same order. Version: 1.12.0 Category: NEW FEATURES Text: Implement "seqnameStyle" replacement method for Seqinfo object. 'seqnameStyle(x) <- style' works on any object with a "seqinfo" replacement method. Version: 1.12.0 Category: NEW FEATURES Text: Add trim,GenomicRanges-method to trim out of bound ranges. Version: 1.12.0 Category: NEW FEATURES Text: Add promoters,GenomicRanges and promoters,GRangesList methods. Version: 1.12.0 Category: NEW FEATURES Text: Add "overlapsAny" methods as a replacement for the deprecated "%in%" methods. Version: 1.12.0 Category: NEW FEATURES Text: Add 'ignore.strand' argument to match,GenomicRanges-method. Version: 1.12.0 Category: NEW FEATURES Text: Add 'with.mapping' argument to "reduce" method for GenomicRanges objects. Version: 1.12.0 Category: NEW FEATURES Text: Add "unname" method to remove dimnames from SummarizedExperiment. Version: 1.12.0 Category: NEW FEATURES Text: Add "cbind" and "rbind" methods for SummarizedExperiment. Version: 1.12.0 Category: NEW FEATURES Text: Add "seqselect", "seqselect<-" and "split" methods for SummarizedExperiment. Version: 1.12.0 Category: NEW FEATURES Text: Add GAlignmentsList class. Version: 1.12.0 Category: NEW FEATURES Text: Add readGAlignmentsList generic and methods. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: resize,GenomicRanges method no longer checks that 'fix' is length-compatible with 'x' when 'x' is length zero. This allows for resize(x, w, fix = "end") without worrying about 'x' being zero-length. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change the behavior of "distance". Previously adjacent ranges had a distance of 1 and overlapping had a distance of 0. Now both adjacent AND overlapping have a distance of 0. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: shift,GenomicRanges-method no longer trims out of bound ranges. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: "distanceToNearest" no longer drops ranges that have no hit but returns 'NA' for 'subjectHits' and 'distance'. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: "genome" is no longer an invalid metadata colname for GenomicRanges objects. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 4x-8x speedup for doing coverage() on a GRanges or GRangesList with many seqlevels. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove ">=", "<", and ">" methods for GenomicRanges objects. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speedup "seqinfo" setters for GenomicRanges and GappedAlignments by avoiding validation when not necessary. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: readGappedAlignments can now pass a BamFile to readBamGappedAlignments. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove unneeded "unique" and "sort" methods for GenomicRanges objects. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change behavior of "match" and "%in%" on GenomicRanges objects to use equality instead of overlap for comparing elements between GenomicRanges objects 'x' and 'table'. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: match,GenomicRanges-method gets the same 'method' argumnet as the "duplicated" method for these objects. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove unneeded "countOverlaps" methods. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: "classNameForDisplay" shortens the name of data type when displayed. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add global options 'showHeadLines' and 'showTailLines' to control the number of head/tails lines displayed in show,GRanges and show,GappedAlignments methods. Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: "distanceToNearest" now returns a Hits object instead of DataFrame. Version: 1.12.0 Category: DEPRECATED AND DEFUNCT Text: Remove defunct countGenomicOverlaps(), grg(), and globalToQuery() Version: 1.12.0 Category: DEPRECATED AND DEFUNCT Text: Defunct previously deprecated '.ignoreElementMetadata' argument of c,GenomicRanges-method. Version: 1.12.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate all "match" and "%in%" methods in the package except for those with the GenomicRanges,GenomicRanges signature. Version: 1.12.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate "resolveHits" methods. Version: 1.12.0 Category: BUG FIXES Text: Several bug fixes to "nearest". Version: 1.12.0 Category: BUG FIXES Text: Output of "findSpliceOverlaps" now displays 'NA' for ranges with no hits. Version: 1.10.0 Category: NEW FEATURES Text: SummarizedExperiment gains direct GRanges / GRangesList interface to rowData. Version: 1.10.0 Category: NEW FEATURES Text: Add "distanceToNearest" method for GenomicRanges objects. Version: 1.10.0 Category: NEW FEATURES Text: SummarizedExperiment class can now be subset by row when there are no 'columns', and by column when there are no 'rows'. Version: 1.10.0 Category: NEW FEATURES Text: Add 'drop.D.ranges' argument to coverage,GappedAlignments and coverage,GappedAlignmentPairs methods. Version: 1.10.0 Category: NEW FEATURES Text: findOverlaps() now supports 'select="last"' and 'select="arbitrary"' (in addition to 'select="all"' and 'select="first"') on GenomicRanges objects. Version: 1.10.0 Category: NEW FEATURES Text: summarizeOverlaps(..., mode="IntersectionStrict") now handles circular chromosomes. A warning is issued and circular chromosomes in 'reads' are omitted from counting. Version: 1.10.0 Category: NEW FEATURES Text: Add disjoin,GRangesList method. Version: 1.10.0 Category: NEW FEATURES Text: Add findSpliceOverlaps() for identifyng ranges (reads) that are compatible with a specific transcript isoform (the non-compatible ranges are analyzed for the presence of novel splice events). Version: 1.10.0 Category: NEW FEATURES Text: Add ngap,GappedAlignmentPairs method. Version: 1.10.0 Category: NEW FEATURES Text: Add introns() generic with methods for GappedAlignments and GappedAlignmentPairs objects. Version: 1.10.0 Category: NEW FEATURES Text: No more arbitrary max of 3 gaps per read in isCompatibleWithSplicing() and isCompatibleWithSkippedExons(). Version: 1.10.0 Category: NEW FEATURES Text: Add findCompatibleOverlaps() and countCompatibleOverlaps(). Version: 1.10.0 Category: NEW FEATURES Text: Passing '...' down through as.data.frame(GRanges, ...) so user can tweak stringsAsFactors default for metadata columns. Version: 1.10.0 Category: NEW FEATURES Text: Add extractSteppedExonRanks(), extractSpannedExonRanks() and extractQueryStartInTranscript() utilities (work with single- and paired-end reads). Version: 1.10.0 Category: NEW FEATURES Text: Add 'flip.query.if.wrong.strand' arg (FALSE by default) to "encodeOverlaps" method for GRangesList objects. Version: 1.10.0 Category: NEW FEATURES Text: Add makeSeqnameIds() low-level utility. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: SummarizedExperiment rowData and assays operations have significant performance improvements. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: mcols() is now the preferred way (over elementMetadata() or values()) to access the metadata columns of a GenomicRanges, GRangesList, GappedAlignments, GappedAlignmentPairs, SummarizedExperiment object, or any Vector object. elementMetadata() and values() might go away at some point in the (not so close) future. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Add "$" and "$<-" methods for GenomicRanges *only*. Provided as a convenience and as the result of strong popular demand. Note that those methods are not consistent with the other "$" and "$<-" methods in the IRanges/GenomicRanges infrastructure, and might confuse some users by making them believe that a GenomicRanges object can be manipulated as a data.frame-like object. It is therefore recommended to use them only interactively, and their use in scripts or packages is discouraged. For the latter, use 'mcols(x)$name' instead of 'x$name'. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: No more warning when doing as(x, "GRanges") on a RangedData object with no "strand" column. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Refactor "[" method for GenomicRanges objects. The new implementation always preserves the names of the selected elements instead of trying to return a GenomicRanges object with unique names. This new behavior is consistent with subsetting of ordinary vectors and other Vector objects defined in IRanges/GenomicRanges. Also modify "seqselect" method for GenomicRanges objects so it also preserves the names of the selected elements (and thus remains consistent with new behavior of "[" method for GenomicRanges objects). Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: No more names on the integer vector returned by "ngap" method for GappedAlignments objects. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Many improvements to the "Overlap encodings" vignette. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove 'param' argument from summarizeOverlaps() generic. Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: Defunct previously deprecated grg() function. Version: 1.10.0 Category: DEPRECATED AND DEFUNCT Text: Defunct previously deprecated countGenomicOverlaps() generic and methods. Version: 1.10.0 Category: BUG FIXES Text: Fix several issues with "precede", "follow", "nearest", and "distance" methods for GenomicRanges objects. Version: 1.10.0 Category: BUG FIXES Text: Fix bug in summarizeOverlaps(..., ignore.strand=TRUE). Version: 1.10.0 Category: BUG FIXES Text: 6x speedup (and a 6x memory footprint reduction) or more when using encodeOverlaps() on big GRangesList objects. Version: 1.10.0 Category: BUG FIXES Text: Fix bug in renameSeqlevels() wrt order of rename vector. Version: 1.10.0 Category: BUG FIXES Text: Fix bug in selectEncodingWithCompatibleStrand(). Version: 1.8.0 Category: NEW FEATURES Text: Add GappedAlignmentPairs class (with accessors first(), last(), left(), right(), seqnames(), strand(), isProperPair()), and readGappedAlignmentPairs() for dealing with paired-end reads. Most of the GappedAlignments functionalities (e.g. coercion to GRangesList, "findOverlaps" and related methods, "coverage", etc...) work on a GappedAlignmentPairs object. Version: 1.8.0 Category: NEW FEATURES Text: Add encodeOverlaps,GRangesList,GRangesList,missing and related utilities flipQuery(), selectEncodingWithCompatibleStrand(), isCompatibleWithSplicing(), isCompatibleWithSkippedExons() and extractSkippedExonRanks(). Version: 1.8.0 Category: NEW FEATURES Text: Add 'order.as.in.query' arg to grglist() and rglist(). Version: 1.8.0 Category: NEW FEATURES Text: SummarizedExperiment gains direct access to colData columns with $, $<-, [[, and [[<- methods Version: 1.8.0 Category: NEW FEATURES Text: Add map,GenomicRanges,GRangesList and map,GenomicRanges,GappedAlignments methods. These allow mapping from genome space to transcript space, and genome space to read space, respectively. Version: 1.8.0 Category: NEW FEATURES Text: Add seqinfo methods (and friends) for RangedData, RangesList, and other IRanges data structures. These use metadata(x)$seqinfo. Version: 1.8.0 Category: NEW FEATURES Text: Add disjointBins,GenomicRanges. Version: 1.8.0 Category: NEW FEATURES Text: Add score,GRangesList and score,GenomicRanges (gets the score column like for RangedData). Version: 1.8.0 Category: NEW FEATURES Text: Add RangedDataList -> GenomicRangesList coercion. Version: 1.8.0 Category: NEW FEATURES Text: Add RleViewsList -> GRanges coercion. Version: 1.8.0 Category: NEW FEATURES Text: Add pintersect,GRangesList,GRangesList Version: 1.8.0 Category: NEW FEATURES Text: Add stack,GenomicRangesList Version: 1.8.0 Category: NEW FEATURES Text: ignore.strand argument now more uniformly supported on set operations. Version: 1.8.0 Category: NEW FEATURES Text: Add Ops,GenomicRanges (from rtracklayer). Version: 1.8.0 Category: NEW FEATURES Text: Add strand,Rle (only logical-Rle is supported). Version: 1.8.0 Category: NEW FEATURES Text: Add compare,GenomicRanges Version: 1.8.0 Category: NEW FEATURES Text: Add 'drop.empty.ranges' arg (FALSE by default) to low-level cigar utilities cigarToIRanges(), cigarToIRangesListByAlignment(), and cigarToIRangesListByRName(). Version: 1.8.0 Category: NEW FEATURES Text: Add 'reduce.ranges' arg to cigarToIRangesListByAlignment(). Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: grglist,GappedAlignments now carries over metadata columns. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Names are no longer forced to be unique when unlisting a GRangesList with use.names=TRUE. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: seqnames() is now preferred over rname() on a GappedAlignments object. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: cigarToIRangesListByAlignment() now returns a CompressedIRangesList instead of CompressedNormalIRangesList. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Low-level CIGAR utilities now ignore CIGAR operation P (instead of trowing an error). Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The 'weight' arg in "coverage" method for GenomicRanges objects now can also be a single string naming a column in elementMetadata(x). Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Ranges outside the sequences bounds of the underlying sequences are now accepted (with a warning) in GenomicRanges/GRangesList/GappedAlignments objects. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: When called with 'ignore.strand=TRUE', the "range" and "disjoin" methods for GenomicRanges objects now behave like if they set the strand of the input to "*" before they do any computation. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: When called with 'ignore.strand=TRUE', "reduce" method for GenomicRanges objects, and "union", "intersect" and "setdiff" methods for GRanges objects now set the strand of their arguments to "*" prior to any computation. Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: No more mangling of the names when combining GRanges objects ("c" method for GRanges objects was trying to return unique names). Version: 1.8.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove isCircularWithKnownLength() generic and methods (nobody knows, uses, or needs this). Version: 1.8.0 Category: BUG FIXES Text: flank,GRangesList no longer forces 'use.names' to TRUE and 'both' to FALSE. Version: 1.8.0 Category: BUG FIXES Text: range,GenomicRanges was broken when object had no ranges Version: 1.8.0 Category: BUG FIXES Text: Fix integer overflow issue that can occur in cigarQNarrow() or cigarQNarrow() when the cigar vector is very long. Version: 1.6.0 Category: NEW FEATURES Text: seqlevels() and seqinfo() setters have a new arg ('force', default is FALSE) to force dropping sequence levels currently in use. Version: 1.6.0 Category: NEW FEATURES Text: Seqinfo objects now have a genome column that can be accessed with genome() getter/setter. Version: 1.6.0 Category: NEW FEATURES Text: "pgap" method for c(x="GRanges", y="GRanges"). Version: 1.6.0 Category: NEW FEATURES Text: Add comparison (==, <=, duplicated, unique, etc...) and ordering (order, sort, rank) methods for GenomicRanges objects. Version: 1.6.0 Category: NEW FEATURES Text: Add "flank" method for GRangesList objects. Version: 1.6.0 Category: NEW FEATURES Text: Add "isDisjoint" and "restrict" methods for GRanges and GRangesList objects. Version: 1.6.0 Category: NEW FEATURES Text: Add GRangesList constructor makeGRangesListFromFeatureFragments(). Version: 1.6.0 Category: NEW FEATURES Text: Add "names" and "names<-" methods for GappedAlignments objects. Version: 1.6.0 Category: NEW FEATURES Text: Add 'ignore.strand' arg to a number of methods: - findOverlaps,GRangesList,RangesList - findOverlaps,GappedAlignments,ANY - findOverlaps,ANY,GappedAlignments Version: 1.6.0 Category: NEW FEATURES Text: 'shift' and 'weight' arguments of "coverage" method for GenomicRanges objects now can be numeric vectors in addition to lists. Version: 1.6.0 Category: NEW FEATURES Text: Add "c" method for GappedAlignments objects. Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: readGappedAlignments() supports 2 new arguments: (1) 'use.names' (default is FALSE) for using the query template names (QNAME field in a SAM/BAM file) to set the names of the returned object, and (2) 'param' (default is NULL, otherwise a ScanBamParam object) for controlling what fields and which records are imported. readGappedAlignments() doesn't support the 'which' arg anymore. Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The names of a GRanges/GRangesList/GappedAlignments object are not required to be unique anymore. Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: By default, the rownames are not set anymore on the DataFrame returned by elementMetadata() on a GRanges/GRangesList/GappedAlignments object. Version: 1.6.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 'width' arg of "coverage" method for GenomicRanges objects now must be NULL or numeric vector (instead of NULL or list). Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate countGenomicOverlaps() in favor of summarizeOverlaps(). Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Deprecate grg() in favor of granges(). Version: 1.6.0 Category: BUG FIXES Text: Fix bug in "pintersect" methods operating on GappedAlignments objects.