r-bioc-genomicranges 1.16.4-2 / usr / lib / R / site-library / GenomicRanges / NEWS

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-LEVEL 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-LEVEL 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-LEVEL 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
      control the number of head/tails lines displayed in
      show,GRanges and show,GappedAlignments methods. 

    o "distanceToNearest" now returns a Hits object instead of DataFrame.

DEPRECATED AND DEFUNCT

    o Remove defunct countGenomicOverlaps(), grg(), and globalToQuery()

    o Defunct previously deprecated '.ignoreElementMetadata' argmuent
      of c,GenomicRanges-method.
 
    o Deprecate all "match" and "%in%" methods in the package except for
      those with the GenomicRanges,GenomicRanges signature.

    o Deprecate "resolveHits" methods.
 
BUG FIXES

    o Several bug fixes to "nearest". 

    o Output of "findSpliceOverlaps" now displays 'NA' for ranges with 
      no hits.


CHANGES IN VERSION 1.10.0
-------------------------

NEW FEATURES

    o SummarizedExperiment gains direct GRanges / GRangesList
      interface to rowData.

    o Add "distanceToNearest" method for GenomicRanges objects.

    o SummarizedExperiment class can now be subset by row when there are no
      'columns', and by column when there are no 'rows'.

    o Add 'drop.D.ranges' argument to coverage,GappedAlignments and
      coverage,GappedAlignmentPairs methods.

    o findOverlaps() now supports 'select="last"' and 'select="arbitrary"' (in
      addition to 'select="all"' and 'select="first"') on GenomicRanges
      objects.

    o summarizeOverlaps(..., mode="IntersectionStrict") now handles circular
      chromosomes. A warning is issued and circular chromosomes in 'reads' are
      omitted from counting.

    o Add disjoin,GRangesList method.

    o 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).

    o Add ngap,GappedAlignmentPairs method.

    o Add introns() generic with methods for GappedAlignments and
      GappedAlignmentPairs objects.

    o No more arbitrary max of 3 gaps per read in isCompatibleWithSplicing()
      and isCompatibleWithSkippedExons(). 

    o Add findCompatibleOverlaps() and countCompatibleOverlaps().

    o Passing '...' down through as.data.frame(GRanges, ...) so user can tweak
      stringsAsFactors default for metadata columns.

    o Add extractSteppedExonRanks(), extractSpannedExonRanks() and
      extractQueryStartInTranscript() utilities (work with single- and
      paired-end reads).

    o Add 'flip.query.if.wrong.strand' arg (FALSE by default) to
      "encodeOverlaps" method for GRangesList objects.

    o Add makeSeqnameIds() low-level utility.

SIGNIFICANT USER-LEVEL CHANGES

    o SummarizedExperiment rowData and assays operations have
      significant performance improvements.

    o 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.

    o 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'.

    o No more warning when doing as(x, "GRanges") on a RangedData object with
      no "strand" column.

    o 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).

    o No more names on the integer vector returned by "ngap" method for
      GappedAlignments objects.

    o Many improvements to the "Overlap encodings" vignette.

    o Remove 'param' argument from summarizeOverlaps() generic.

DEPRECATED AND DEFUNCT

    o Defunct previously deprecated grg() function.

    o Defunct previously deprecated countGenomicOverlaps() generic and methods.

BUG FIXES

    o Fix several issues with "precede", "follow", "nearest", and "distance"
      methods for GenomicRanges objects.

    o Fix bug in summarizeOverlaps(..., ignore.strand=TRUE).

    o 6x speedup (and a 6x memory footprint reduction) or more when using
      encodeOverlaps() on big GRangesList objects.

    o Fix bug in renameSeqlevels() wrt order of rename vector.

    o Fix bug in selectEncodingWithCompatibleStrand().


CHANGES IN VERSION 1.8.0
------------------------

NEW FEATURES

    o 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.

    o Add encodeOverlaps,GRangesList,GRangesList,missing and related utilities
      flipQuery(), selectEncodingWithCompatibleStrand(),
      isCompatibleWithSplicing(), isCompatibleWithSkippedExons() and
      extractSkippedExonRanks().

    o Add 'order.as.in.query' arg to grglist() and rglist().

    o SummarizedExperiment gains direct access to colData columns with
      $, $<-, [[, and [[<- methods

    o 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.
    
    o Add seqinfo methods (and friends) for RangedData, RangesList,
      and other IRanges data structures. These use metadata(x)$seqinfo.

    o Add disjointBins,GenomicRanges.

    o Add score,GRangesList and score,GenomicRanges (gets the score column
      like for RangedData).
    
    o Add RangedDataList -> GenomicRangesList coercion.

    o Add RleViewsList -> GRanges coercion.

    o Add pintersect,GRangesList,GRangesList

    o Add stack,GenomicRangesList
    
    o ignore.strand argument now more uniformly supported on set operations.

    o Add Ops,GenomicRanges (from rtracklayer).

    o Add strand,Rle (only logical-Rle is supported).

    o Add compare,GenomicRanges

    o Add 'drop.empty.ranges' arg (FALSE by default) to low-level cigar
      utilities cigarToIRanges(), cigarToIRangesListByAlignment(), and
      cigarToIRangesListByRName().

    o Add 'reduce.ranges' arg to cigarToIRangesListByAlignment().
 
SIGNIFICANT USER-LEVEL CHANGES

    o grglist,GappedAlignments now carries over metadata columns.

    o Names are no longer forced to be unique when unlisting a
      GRangesList with use.names=TRUE.

    o seqnames() is now preferred over rname() on a GappedAlignments object.

    o cigarToIRangesListByAlignment() now returns a CompressedIRangesList
      instead of CompressedNormalIRangesList.

    o Low-level CIGAR utilities now ignore CIGAR operation P (instead of
      trowing an error).

    o The 'weight' arg in "coverage" method for GenomicRanges objects now
      can also be a single string naming a column in elementMetadata(x).

    o Ranges outside the sequences bounds of the underlying sequences are now
      accepted (with a warning) in GenomicRanges/GRangesList/GappedAlignments
      objects.

    o 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.

    o 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.

    o No more mangling of the names when combining GRanges objects ("c" method
      for GRanges objects was trying to return unique names).

    o Remove isCircularWithKnownLength() generic and methods (nobody knows,
      uses, or needs this).

BUG FIXES

    o flank,GRangesList no longer forces 'use.names' to TRUE and 'both' to
      FALSE.

    o range,GenomicRanges was broken when object had no ranges

    o Fix integer overflow issue that can occur in cigarQNarrow() or
      cigarQNarrow() when the cigar vector is very long.


CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o seqlevels() and seqinfo() setters have a new arg ('force', default is
      FALSE) to force dropping sequence levels currently in use.

    o Seqinfo objects now have a genome column that can be accessed with
      genome() getter/setter.

    o "pgap" method for c(x="GRanges", y="GRanges").

    o Add comparison (==, <=, duplicated, unique, etc...) and ordering
      (order, sort, rank) methods for GenomicRanges objects.

    o Add "flank" method for GRangesList objects.

    o Add "isDisjoint" and "restrict" methods for GRanges and GRangesList
      objects.

    o Add GRangesList constructor makeGRangesListFromFeatureFragments().

    o Add "names" and "names<-" methods for GappedAlignments objects.

    o Add 'ignore.strand' arg to a number of methods:
        - findOverlaps,GRangesList,RangesList
        - findOverlaps,GappedAlignments,ANY
        - findOverlaps,ANY,GappedAlignments

    o 'shift' and 'weight' arguments of "coverage" method for GenomicRanges
      objects now can be numeric vectors in addition to lists.

    o Add "c" method for GappedAlignments objects.

SIGNIFICANT USER-VISIBLE CHANGES

    o 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.

    o The names of a GRanges/GRangesList/GappedAlignments object are not
      required to be unique anymore.

    o By default, the rownames are not set anymore on the DataFrame returned
      by elementMetadata() on a GRanges/GRangesList/GappedAlignments object.

    o 'width' arg of "coverage" method for GenomicRanges objects now must be
      NULL or numeric vector (instead of NULL or list).

DEPRECATED AND DEFUNCT

    o Deprecate countGenomicOverlaps() in favor of summarizeOverlaps().

    o Deprecate grg() in favor of granges().

BUG FIXES

    o Fix bug in "pintersect" methods operating on GappedAlignments objects.