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NEWS
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CHANGES IN VERSION 1.56.0
-------------------------
NEW FEATURES
o Add terminators() method, same as promoters() but for terminator regions.
BUG FIXES
o 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
CHANGES IN VERSION 1.54.0
-------------------------
NEW FEATURES
o Add 'ignore.strand' arg to gaps() method for GenomicRanges objects.
BUG FIXES
o Small tweaks to GRanges() constructor and to coercion from GPos
to GRanges.
CHANGES IN VERSION 1.52.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o 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.
CHANGES IN VERSION 1.50.0
-------------------------
- No changes in this version.
CHANGES IN VERSION 1.48.0
-------------------------
NEW FEATURES
o Add subtract() for subtracting a set of genomic ranges from a GRanges
object. This is similar to bedtools subtract.
o Add 'na.rm' argument to makeGRangesFromDataFrame().
DEPRECATED AND DEFUNCT
o Remove the GenomicRangesList() constructor. This constructor got
deprecated in BioC 3.10 and defunct in BioC 3.13.
BUG FIXES
o Make sure promoters() works on GPos objects.
CHANGES IN VERSION 1.46.0
-------------------------
- No changes in this version.
CHANGES IN VERSION 1.44.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Replace KEGG.db usage with KEGGREST in vignettes and examples.
DEPRECATED AND DEFUNCT
o The GenomicRangesList() constructor is now defunct (got deprecated in
BioC 3.10).
CHANGES IN VERSION 1.42.0
-------------------------
NEW FEATURES
o Add nearestKNeighbors() method for GenomicRanges derivatives.
o 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.
CHANGES IN VERSION 1.40.0
-------------------------
NEW FEATURES
o Add trim() method for GRangesList objects.
CHANGES IN VERSION 1.38.0
-------------------------
NEW FEATURES
o 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().
o GPos objects now can hold names
o Coercion to GPos now propagates the names
o Add GRangesFactor class (Factor derivative). See ?GRangesFactor
SIGNIFICANT USER-VISIBLE CHANGES
o Export from_GPos_to_GRanges()
o Some reorgnization of the GenomicRangesList hierarchy (see commit
f988a5a9).
o Swap order of arguments 'seqlengths' and 'seqinfo' of the GRanges()
constructor so now the latter comes before the former.
DEPRECATED AND DEFUNCT
o Remove findOverlaps, seqnames, and seqinfo<- methods for RangedData
objects. These methods were deprecated in BioC 3.8 and defunct in
BioC 3.9.
BUG FIXES
o Coercion from RangesList to GRanges is more robust to seqlevel
differences
o Fix bug in isSmallGenome() (introduced by change in sum() in R >= 3.5)
CHANGES IN VERSION 1.36.0
-------------------------
NEW FEATURES
o findOverlaps() now supports type="equal" on GRangesList objects
DEPRECATED AND DEFUNCT
o After being deprecated in BioC 3.8, the seqinfo() setter, seqnames(),
and findOverlaps() are now defunct on RangedData objects.
CHANGES IN VERSION 1.34.0
-------------------------
NEW FEATURES
o 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")
DEPRECATED AND DEFUNCT
o 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.
BUG FIXES
o Make [[, as.list(), lapply(), and unlist() fail more graciously on
a GenomicRanges object.
o Make "show" methods for GenomicRanges and GPos objects robust to
special metadata column names like "stringsAsFactors".
o Export the "update" method for GRanges objects. This addresses
https://github.com/Bioconductor/GenomicRanges/issues/7
CHANGES IN VERSION 1.32.0
-------------------------
NEW FEATURES
o 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.
SIGNIFICANT USER-VISIBLE CHANGES
o 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).
o 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.
o GenomicRangesList is now a virtual class (like IntegerRangesList is).
o 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.
o Improve performance of nearest(), precede(), and follow() on a GRanges
object.
o Improve performance of coverage() on a GPos object.
o 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).
o 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.
BUG FIXES
o 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).
o Fix bug in nearest() when an unstranded range in 'query' precedes or
follows more than one range in 'subject'.
CHANGES IN VERSION 1.30.0
-------------------------
NEW FEATURES
o Support GPos-based GRangesList objects.
o Add 'na.rm' argument to binnedAverage().
SIGNIFICANT USER-VISIBLE CHANGES
o 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.
o GPos now extends GRanges but with a ranges slot that must be an IPos
object. Update "old" GPos objects with updateObject().
o Move pos() generic to IRanges package.
o Move rglist() generic to IRanges package.
o Rename GenomicRangesORmissing and GenomicRangesORGRangesList classes ->
GenomicRanges_OR_missing and GenomicRanges_OR_GRangesList, respectively.
o Remove "seqinfo" method for RangesList objects.
o Remove "stack" method for GenomicRangesList objects.
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 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.
o '$' completion on GenomicRanges works in RStudio.
o Minor tweaks to conversion from character to GRanges and reverse
conversion.
CHANGES IN VERSION 1.28.0
-------------------------
NEW FEATURES
o 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).
o seqlevels() setter now supports "fine" and "tidy" pruning modes on
GRangesList objects (in addition to "coarse" mode, which is the default).
o "range" methods now have a 'with.revmap' argument (like "reduce" and
"disjoin" methods).
o Add a bunch of range-oriented methods for GenomicRangesList objects.
SIGNIFICANT USER-VISIBLE CHANGES
o Some changes/improvements to "precede" and "follow" methods for
GenomicRanges objects motivated by discussion on support site:
https://support.bioconductor.org/p/90664/
o 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'.
DEPRECATED AND DEFUNCT
o Argument 'force' of seqinfo() and seqlevels() setters is deprecated in
favor of new and more flexible 'pruning.mode' argument.
BUG FIXES
o Fix severe performance regression introduced in Bioconductor 3.3 in
"intersect" and "setdiff" methods for GRangesList objects. Thanks to
Jens Reeder <reeder.jens@gene.com> for catching and reporting this.
CHANGES IN VERSION 1.26.0
-------------------------
NEW FEATURES
o Add 'with.revmap' argument to "reduce" method for GRangesList objects.
o Add 'with.revmap' argument to various "disjoin" methods.
o makeGRangesFromDataFrame() now tries to turn the "start" and "end"
columns of the input data frame into numeric vectors if they are not
already.
o Add makeGRangesListFromDataFrame() function.
o Add "summary" method for GenomicRanges objects.
o 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.
o Add 'use.mcols' arguments to the "ranges" methods for GPos objects.
SIGNIFICANT USER-VISIBLE CHANGES
DEPRECATED AND DEFUNCT
BUG FIXES
o Fix bug in distanceToNearest() related to ranges starting at zero.
o Fix GRanges(Seqinfo()).
CHANGES IN VERSION 1.24.0
-------------------------
NEW FEATURES
o 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.
o 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.
o Add "is.unsorted" method for GenomicRanges objects (contributed by Pete
Hickey).
o 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.
o Add "selfmatch" method for GenomicRanges objects.
o Add "union" method for GRangesList objects.
SIGNIFICANT USER-VISIBLE CHANGES
o Remove old SummarizedExperiment class from the GenomicRanges package
(this class is now defined in the SummarizedExperiment package).
o 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<-"
o 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).
o 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.
o Use DESeq2 instead of DESeq in the vignettes (better late than never).
DEPRECATED AND DEFUNCT
o Remove GIntervalTree class and methods (were defunct in BioC 3.2).
o Remove mapCoords() and pmapCoords() (were defunct in BioC 3.2).
CHANGES IN VERSION 1.22.0
-------------------------
NEW FEATURES
o 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:+'.
o Add facilities for manipulating "genomic variables": bindAsGRanges(),
mcolAsRleList(), and binnedAverage(). See ?genomicvars for more
information.
o Add "narrow" method for GRangesList objects.
o 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.
o Add 'ignore.strand' argument to "range" and "reduce" methods for
GRangesList objects.
o Add coercion from SummarizedExperiment to RangedSummarizedExperiment
(also available via updateObject()). See 1st item in DEPRECATED AND
DEFUNCT section below for more information about this.
o GNCList objects are now subsettable.
o "coverage" methods now accept 'shift' and 'weight' supplied as an Rle.
SIGNIFICANT USER-VISIBLE CHANGES
o Modify behavior of "*" strand in precede() / follow() to mimic
'ignore.strand=TRUE'.
o 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'.
o 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).
o GRanges() constructor no more mangles the names of the supplied metadata
columns (e.g. if the column is "_tx_id").
o makeGRangesFromDataFrame() now accepts "." in strand column (treated as
"*").
o GNCList() constructor now propagates the metadata columns.
o Remove "seqnames" method for RangesList objects.
DEPRECATED AND DEFUNCT
o 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).
o makeSummarizedExperimentFromExpressionSet() and related stuff was moved
to the new SummarizedExperiment package.
o After being deprecated in BioC 3.1, the rowData accessor is now defunct
(replaced with the rowRanges accessor).
o After being deprecated in BioC 3.1, GIntervalTree objects and the
"intervaltree" algorithm in findOverlaps() are now defunct.
o After being deprecated in BioC 3.1, mapCoords() and pmapCoords() are
now defunct.
BUG FIXES
o 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.
CHANGES IN VERSION 1.20.0
-------------------------
NEW FEATURES
o Add coercion methods to go back and forth between ExpressionSet and
SummarizedExperiment.
o Add 'assayNames', 'assayNames<-' for SummarizedExperiment
o assays() supports arrays of up to 4 dimensions.
o 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).
o All "findOverlaps" methods now support 'select' equal "last" or
"arbitrary" (in addition to "all" and "first").
o Add absoluteRanges() and relativeRanges() to transform back and forth
between absolute and relative genomic ranges.
SIGNIFICANT USER-VISIBLE CHANGES
o Renamed 'rowData' and 'rowData<-' -> 'rowRanges', 'rowRanges<-'.
Old names still work but are deprecated.
o 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.
o The GRanges() constructor now propagates the metadata cols that are on
'ranges' if no metadata cols are explicitly passed to the constructor.
DEPRECATED AND DEFUNCT
o Deprecated 'rowData' and 'rowData<-' in favor of 'rowRanges' and
'rowRanges<-'.
o Deprecated mapCoords() and pmapCoords(). They're replaced by
mapToTranscripts() and pmapToTranscripts() from the GenomicFeatures
package and mapToAlignments() and pmapToAlignments() from the
GenomicAlignments package.
o Deprecated GIntervalTree objects.
o Removed "map" and "splitAsListReturnedClass" methods (were defunct in
GenomicRanges 1.18.0).
o Removed makeSeqnameIds() (was defunct in GenomicRanges 1.18.0).
o Removed 'with.mapping' argunment from "reduce" methods (was defunct in
GenomicRanges 1.18.0).
BUG FIXES
o Fix 'findOverlaps(..., type="start")' on GRangesList objects which has
been broken for years.
o Fix self overlap search on a GRanges object when 'ignore.strand=TRUE'
(i.e. 'findOverlaps(gr, ignore.strand=TRUE)').
CHANGES IN VERSION 1.18.0
-------------------------
NEW FEATURES
o Add 'use.mcols' arg to "ranges" method for GRangesList objects.
o "assays<-" methods may be invoked with 'withDimnames' arg.
o Add mapCoords() generic and methods (replacing map()).
o Add granges,GenomicRanges method.
o Add strand<-,GRangesList,character method for global replacement
(i.e., all strands become 'value').
o Add resize,GRangesList-method.
o Add DelegatingGenomicRanges class and vignette on how to extend
GenomicRanges.
o Document subsetting a named list-like object by a GRanges subscript.
SIGNIFICANT USER-VISIBLE CHANGES
o Modify "show" methods for GRanges and GRangesList objects so
they print a 1-line summary of the seqinfo component.
o Remove as.data.frame,GRangesList-method; use as.data.frame,List.
o "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.
o 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().
o Speed up validation of GenomicRanges objects by 1.2x.
o Speed up trim() on GenomicRanges objects by 1.2x.
o Improve warning when GenomicRanges object contains out-of-bound ranges.
o 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
o Follow renaming of TranscriptDb class to TxDb.
o Replace references to plantsmart21 with plantsmart22.
DEPRECATED AND DEFUNCT
o Defunct map() (skip deprecation). Replace with mapCoords().
BUG FIXES
o [cr]bind,SummarizedExperiment methods respect derived classes.
o assays(se, withDimnames=TRUE) <- value no longer tries to access
a slot 'withDimnames'.
o cbind and rbind,SummarizedExperiment-methods respect derived
classes
o "ranges" method for GRangesList objects should not propagate
inner metadata columns by default.
o GRanges() constructor now preserves the seqlevels in the order
supplied by the user.
o Ensure tileGenome() breakpoints do not extend past end of genome.
o Fix "show" method for GenomicRanges objects when 'showHeadLines'
global option is set to Inf.
o [rc]bind,SummarizeExperiment-methods now compare all elements.
o Remove "==" and "<=" methods for GenomicRanges objects (not needed).
CHANGES IN VERSION 1.16.0
-------------------------
NEW FEATURES
o Add "subset" method for SummarizedExperiment objects.
o Allow DataFrame in SummarizedExperiment assays.
o Add 'use.mcols' arg (FALSE by default) to the granges(), grglist(), and
rglist() generics (a.k.a. the range-squeezer generics).
o Add coercion method from GRangesList to RangesList.
o Add score() setter for GRangesList objects.
o findOverlaps(..., type="within") now works on circular chromosomes.
o Add 'ignore.strand' arg to "sort" method for GRanges objects.
o Support subsetting of a named list-like object *by* a GenomicRanges
subscript.
o Support sort(granges, by = ~ score), i.e., a formula-based interface for
sorting by the mcols.
SIGNIFICANT USER-VISIBLE CHANGES
o 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.
o Rename 'with.mapping' arg -> 'with.revmap' in "reduce" methods. The old
arg name is still working but deprecated.
o Move makeSeqnameIds() function to the new GenomeInfoDb package and rename
it rankSeqlevels(). The old name is still working but deprecated.
o 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.
BUG FIXES
o 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).
CHANGES IN VERSION 1.14.0
-------------------------
NEW FEATURES
o Add coercion from GenomicRangesList to RangedDataList.
o Add "c" method for GAlignmentPairs objects.
o Add coercion from GAlignmentPairs to GAlignmentsList.
o Add 'inter.feature' and 'fragment' arguments to summarizeOverlaps().
o Add seqselect,GAlignments-method.
o Add CIGAR utilities:
explodeCigarOps(), explodeCigarOpLengths()
cigarRangesAlongReferenceSpace(), cigarRangesAlongQuerySpace()
cigarRangesAlongPairwiseSpace(), extractAlignmentRangesOnReference()
cigarWidthAlongReferenceSpace(), cigarWidthAlongQuerySpace()
cigarWidthAlongPairwiseSpace().
o Add seqlevels0() and restoreSeqlevels().
o Add seqlevelsInUse() getter for GRanges, GRangesList, GAlignments
GAlignmentPairs, GAlignmentsList and SummarizedExperiment objects.
o Add update,GAlignments method.
o Add GIntervalTree class.
o Add coercion from GAlignmentPairs to GAlignments.
o Add sortSeqlevels().
o Add tileGenome().
o Add makeGRangesFromDataFrame() and coercion from data.frame or DataFrame
to GRanges.
SIGNIFICANT USER-VISIBLE CHANGES
o Renaming (with aliases from old to new names):
- classes
GappedAlignments -> GAlignments
GappedAlignmentPairs -> GAlignmentPairs
- functions
GappedAlignments() -> GAlignments()
GappedAlignmentPairs() -> GAlignmentPairs()
readGappedAlignments() -> readGAlignments()
readGappedAlignmentPairs() -> readGAlignmentPairs()
o Remove 'asProperPairs' argument to readGAlignmentsList().
o Modify "show" method for Seqinfo object to honor showHeadLines
and showTailLines global options.
o 50x speedup or more when merging 2 Seqinfo objects, 1 very small
and 1 very big.
o Add dependency on new XVector package.
o Enhanced examples for renaming seqlevels in seqlevels-utils.Rd.
o More efficient reference class constructor for 'assays'
slot of SummarizedExperiment objects.
o 'colData' slot of SummarizedExperiment produced from call to
summarizedOverlaps() now holds the class type and length of 'reads'.
o 4x speedup to cigarToRleList().
o Relax SummarizedExperiment class validity.
o Renaming (with aliases from old to new names):
cigarToWidth() -> cigarWidthOnReferenceSpace(), and
cigarToQWidth() -> cigarWidthOnQuerySpace().
o Improvements to summarizeOverlaps():
- mode 'Union': 1.5x to 2x speedup
- mode 'IntersectionNotEmpty': 2x to 8x speedup + memory footprint
reduced by ~ half
o Change default 'use.names' to FALSE for readGAlignmentsList().
o Implement 'type="equal"' for findOverlaps,SummarizedExperiment methods.
o Modify summarizeOverlaps() examples to use 'asMates=TRUE' instead
of 'obeyQname=TRUE'.
o Remove unneeded "window" method for GenomicRanges objects.
o Speed up seqinfo() getter and setter on SummarizedExperiment objects
and derivatives (e.g. VCF) by using direct access to 'rowData' slot.
o coverage,GenomicRanges method now uses .Ranges.coverage() when
using the defaults for 'shift' and 'width'.
o Remove restriction that metadata column names must be different on
a GRangesList and the unlisted GRanges.
o GenomicRangesUseCases vignette has been redone and renamed
to GenomicRangesHOWTOs.
DEPRECATED AND DEFUNCT
o Defunct all "match" and "%in%" methods in the
package except for those with the GenomicRanges,GenomicRanges signature.
o Deprecate GappedAlignment*:
- GappedAlignments and GappedAlignmentPairs classes
- GappedAlignments() and GappedAlignmentPairs() constructors
- readGappedAlignments() and readGappedAlignmentPairs() functions
o Deprecate cigar util functions:
cigarToWidth(), cigarToQWidth(), cigarToIRanges()
splitCigar(), cigarToIRanges(), cigarToIRangesListByAlignment()
cigarToIRangesListByRName(), cigarToWidth(), cigarToQWidth()
cigarToCigarTable(), summarizeCigarTable()
o Deprecate seqselect().
BUG FIXES
o Fix bug in c,GAlignments for case when objects were unnamed.
o Fix bug in flank,GenomicRanges (when 'ignore.strand=TRUE'
'start' was being set to TRUE).
o Fix bug in behavior of summarizeOverlaps() count mode
'IntersectionNotEmpty' when 'inter.features=FALSE'. Shared
regions are now removed before counting.
o Fix bug in cigarToIRangesListByAlignment() when 'flag' is
supplied and indicates some reads are unmapped.
o Fix bug in summarizeOverlaps(..., mode='IntersectionNotEmpty')
when 'features' has '-' and '+' elements and 'ignore.strand=TRUE'.
o match,GenomicRanges,GenomicRanges method now handles properly objects
with seqlevels not in the same order.
CHANGES IN VERSION 1.12.0
-------------------------
NEW FEATURES
o Implement "seqnameStyle" replacement method for Seqinfo object.
'seqnameStyle(x) <- style' works on any object with a "seqinfo"
replacement method.
o Add trim,GenomicRanges-method to trim out of bound ranges.
o Add promoters,GenomicRanges and promoters,GRangesList methods.
o Add "overlapsAny" methods as a replacement for the deprecated
"%in%" methods.
o Add 'ignore.strand' argument to match,GenomicRanges-method.
o Add 'with.mapping' argument to "reduce" method for GenomicRanges
objects.
o Add "unname" method to remove dimnames from SummarizedExperiment.
o Add "cbind" and "rbind" methods for SummarizedExperiment.
o Add "seqselect", "seqselect<-" and "split" methods for
SummarizedExperiment.
o Add GAlignmentsList class.
o Add readGAlignmentsList generic and methods.
SIGNIFICANT USER-VISIBLE CHANGES
o 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.
o 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.
o shift,GenomicRanges-method no longer trims out of bound ranges.
o "distanceToNearest" no longer drops ranges that have no hit
but returns 'NA' for 'subjectHits' and 'distance'.
o "genome" is no longer an invalid metadata colname for GenomicRanges
objects.
o 4x-8x speedup for doing coverage() on a GRanges or GRangesList with
many seqlevels.
o Remove ">=", "<", and ">" methods for GenomicRanges objects.
o Speedup "seqinfo" setters for GenomicRanges and GappedAlignments
by avoiding validation when not necessary.
o readGappedAlignments can now pass a BamFile to readBamGappedAlignments.
o Remove unneeded "unique" and "sort" methods for GenomicRanges objects.
o Change behavior of "match" and "%in%" on GenomicRanges objects to use
equality instead of overlap for comparing elements between GenomicRanges
objects 'x' and 'table'.
o match,GenomicRanges-method gets the same 'method' argumnet as the
"duplicated" method for these objects.
o Remove unneeded "countOverlaps" methods.
o "classNameForDisplay" shortens the name of data type when displayed.
o Add global options 'showHeadLines' and 'showTailLines' to