r-bioc-iranges 1.22.10-1 / usr / lib / R / site-library / IRanges / NEWS

CHANGES IN VERSION 1.20.0
-------------------------

NEW FEATURES

    o Add IntervalForest class from Hector Corrada Bravo.

    o Add a FilterMatrix class, for holding the results of multiple filters.

    o Add selfmatch() as a faster equivalent of 'match(x, x)'.

    o Add "c" method for Views objects (only combine objects with same
      subject).

    o Add coercion from SimpleRangesList to SimpleIRangesList.

    o Add an `%outside%` that is the opposite of `%over%`.

    o Add validation of length() and names() of Vector objects.

    o Add "duplicated" and "table" methods for Vector objects.

    o Add some split methods that dispatch to splitAsList() even when only
      'f' is a Vector.

    o Add set methods (setdiff, intersect, union) for Rle.

    o Add anyNA methods for Rle and Vector.

    o Add support for subset(), with(), etc on Vector objects,
      where the expressions are evaluated in the scope of the
      mcols and fixed columns. For symbols that should resolve
      in the calling frame, it is supported and encouraged to escape
      them with bquote-style ".(x)".

    o Add "tile" generic and methods for partitioning a ranges object
      into tiles; useful for iterating over subregions.

SIGNIFICANT USER-VISIBLE CHANGES

    o All functionalities related to XVector objects have been moved to the
      new XVector package.

    o Refine how isDisjoint() handles empty ranges.

    o Remove 'keepLength' argument from "window<-" methods.

    o unlist( , use.names=FALSE) on a CompressedSplitDataFrameList object
      now preserves the rownames of the list elements, which is more
      consistent with what unlist() does on other CompressedList objects.

    o Splitting a list by a Vector just yields a list, not a List.

    o The rbind,DataFrame method now handles the case where Rle and vector
      columns need to be combined (assuming an equivalence between Rle and
      vector). Also the way the result DataFrame is constructed was changed
      (avoids undesirable coercions and should be faster).

    o as.data.frame.DataFrame now passes 'stringsAsFactors=FALSE' and
      'check.names=!optional' to the underlying data.frame() call.
      as(x,"DataFrame") sets 'optional=TRUE' when delegating. Most places
      where we called as.data.frame(), we now call 'as(x,"data.frame")'.

    o The [<-,DataFrame method now coerces column sub-replacement value to
      class of column when the column already exists.

    o DataFrame() now automatically derives rownames (from the first argument
      that has some). This is a fairly significant change in behavior, but it
      probably does better match user behavior.

    o Make sure that SimpleList objects are coerced to a DataFrame with a
      single column. The automatic coecion methods created by the methods
      package were trying to create a DataFrame with one column per element,
      because DataFrame extends SimpleList.

    o Change default to 'compress=TRUE' for RleList() constructor.

    o tapply() now handles the case where only INDEX is a Vector (e.g.
      an Rle object).

    o Speedup coverage() in the "tiling case" (i.e. when 'x' is a tiling
      of the [1, width] interval). This makes it much faster to turn into an
      Rle a coverage loaded from a BigWig, WIG or BED as a GRanges object.

    o Allow logical Rle return values from filter rules.

    o FilterRules no longer requires its elements to be named.

    o The select,Vector method now returns a DataFrame even when a single
      column is selected.

    o Move is.unsorted() generic to BiocGenerics.

DEPRECATED AND DEFUNCT

    o Deprecate seqselect() and subsetByRanges().

    o Deprecate 'match.if.overlap' arg of "match" method for Ranges objects.

    o "match" and "%in%" methods that operate on Views, ViewsList, RangesList,
      or RangedData objects (20 methods in total) are now defunct.

    o Remove previously defunct tofactor().

BUG FIXES

    o The subsetting code for Vector derivatives was substancially refactored.
      As a consequence, it's now cleaner, simpler, and [ and [[ behave more
      consistently across Vector derivatives. Some obscure long-standing bugs
      have been eliminated and the code can be slightly faster in some
      circumstances.

    o Fix bug in findOverlaps(); zero-width ranges in the query no longer
      produce hits ever (regardless of 'maxgap' and 'minoverlap' values).

    o Correctly free memory allocated for linked list of results compiled for
      findOverlap(select="all").

    o Various fixes for AsIs and DataFrames.

    o Allow zero-row replacement values in [<-,DataFrame.

    o Fix long standing segfault in "[" method for Rle objects (when doing
      Rle()[0]).

    o "show" methods now display its most specific class when a column or
      slot is an S3 object for which class() returns more than one class.

    o "show" methods now display properly cells that are arrays.

    o Fix the [<-,DataFrame method for when a value DataFrame has matrix
      columns.

    o Fix ifelse() for when one or more of the arguments are Rle objects.

    o Fix coercion from SimpleList to CompressedList via AtomicList
      constructors.

    o Make "show" methods robust to "showHeadLines" and "showTailLines" global
      options set to NA, Inf or non-integer values.

    o Fix error condition in eval,FilterRules method.

    o Corrected an error formatting in eval,FilterRules,ANY method.


CHANGES IN VERSION 1.18.0
-------------------------

NEW FEATURES

    o Add global options 'showHeadLines' and 'showTailLines' to
      control the number of head/tails lines displayed by "show" methods
      for Ranges, DataTable, and Hits objects.

    o "subset" method for Vector objects now considers metadata columns.

    o Add classNameForDisplay() generic and use it in all "show" methods
      defined in IRanges and GenomicRanges.

    o as(x, "DataFrame") now works on *any* R object.

    o Add findMatches(), an enhanced version of match() that returns all the
      matches between 'x' and 'table'. The hits are returned in a Hits object.
      Also add countMatches() for counting the number of matches in 'table'
      for each element in 'x'.

    o Add overlapsAny() as a replacement for %in% (now deprecated on
      range-based objects), and %over% and %within% as convenience wrappers
      for overlapsAny(). %over% is the replacement for %in%.

    o Add 'with.mapping' arg to "reduce" methods for IRanges, Ranges, Views,
      RangesList, and CompressedIRangesList objects.

    o Add "order" method for Rle objects.

    o Add subsetByRanges() generic with methods for ANY, NULL, vector, and
      IRanges for now. This is work-in-progress and more methods will be added
      soon. The long term plan is to make this a replacement for seqselect(),
      but with a faster and cleaner implementation.

    o Add promoters() generic with methods for Ranges, RangesList, Views, and
      CompressedIRangesList objects.

    o elementLengths() now works on XVectorList objects (and thus works on
      DNAStringSet objects and family defined in the Biostrings package).
      Note that this is the first step towards having relist() work on XVector
      objects (e.g. DNAString objects) eventhough this is not ready yet.

    o Add "mstack" method for DataFrame objects.

    o Add 'name.var' argument to "stack" method for List objects for naming
      the optional column formed when the elements themselves have named
      elements.

SIGNIFICANT USER-VISIBLE CHANGES

    o "distanceToNearest" methods now return a Hits instead of
      a DataFrame object. 

    o The behavior of distance() has changed. Adjacent and overlapping ranges
      now return a distance of 0L. See ?distance man page for details.
      A temporary warning will be emitted by distance() until the release of
      Bioconductor 2.13.

    o Change arg list of expand() generic: function(x, ...) instead of
      function(x, colnames, keepEmptyRows).

    o Dramatic duplicated() and unique() speedups on CompressedAtomicList
      objects.

    o Significant endoapply() speedup on XVectorList objects (this benefits
      DNAStringSet objects and family defined in the Biostrings package).

    o 2x speedup to "c" method for CompressedList objects.

    o classNameForDisplay() strips 'Simple' or 'Compressed', which affects
      all the "show" methods based on it. So now:

        > IntegerList(1:4, 2:-3)
        IntegerList of length 2
        [[1]] 1 2 3 4
        [[2]] 2 1 0 -1 -2 -3

      instead of:

        > IntegerList(1:4, 2:-3)
        CompressedIntegerList of length 2
        [[1]] 1 2 3 4
        [[2]] 2 1 0 -1 -2 -3

    o Optimization of "[<-" method for Rle objects when no indices are
      selected (just return self).

    o "stack" method for List objects now creates a factor for the optional
      name variable.

    o Evaluating FilterRules now subsets by each filter individually, rather
      than subsetting by all at the end.

    o Optimized which() on CompressedLogicalList objects.

    o All the binary comparison operations (==, <=, etc...) on Ranges objects
      are now using compare() behind the scene. This makes them slightly faster
      and also slightly more memory efficient.

DEPRECATED AND DEFUNCT

    o %in% is now deprecated on range-based objects. Please use %over% instead.
      More precisely:
        - "match" and "%in%" methods that operate on Views, ViewsList,
          RangesList, or RangedData objects (20 methods in total) are now
          deprecated.
        - Behavior of match() and %in% on Ranges objects was changed (and
          will issue a warning) to use equality instead of overlap for
          comparing elements between Ranges objects 'x' and 'table'. The old
          behavior is still available for match() via new 'match.if.overlap'
          arg that is FALSE by default (the arg will be deprecated in BioC 2.13
          and removed in BioC 2.14).

    o tofactor() is now defunct.

    o '.ignoreElementMetadata' argument of "c" method for IRanges objects is
      now defunct.

BUG FIXES

    o Small fix to "unlist" method for CompressedList objects when 'use.names'
      is TRUE and 'x' is a zero-length named List (the zero-length vector
      returned in that case was not named, now it is).

    o "resize" method for Ranges objects now allows zero-length 'fix' when
      'x' is zero-length.

    o Subsetting a Views object now subsets its metadata columns.

    o Names on the vector-like columns of a DataFrame object are now preserved
      when calling DataFrame(), or when coercing to DataFrame, or when
      combining DataFrame objects with rbind().

    o relist() now propagates the names on 'skeleton' when returning
      a SimpleList.

    o Better argument checking in breakInChunks().

    o Fix broken "showAsCell" method for ANY. Now tries to coerce
      uni-dimensional objects to vector instead of data.frame (which never
      worked anyway, due to a bug).

    o Fix long standing bug in "flank" method for Ranges objects: it no longer
      returns an invalid object when NAs are passed thru the 'width' arg.
      Now it's an error to try to do so.

    o Fix issue with some of the "as.env" methods not being able to find the
      environment of the caller.

    o Fix bug in "showAsCell" method for AtomicList objects: now returns
      character(0) instead of NULL on an object of length 0.

    o sort() now drops NA's when 'na.last=NA' on an Rle object (consistent
      with base::sort).

    o table() now handles NA's appropriately on an Rle object.

    o table() now returns all the levels on a factor-Rle object.

    o Fix sub-replacement of Rles when using Ranges as the index.

    o Fix bug in [<- method for DataFrame objects. The fix corrects the way
      a new column created by a subset assignment is filled. Previously, if
      the first row was set, say, to '1', all values in the column were set
      to '1' when they needed to be set to NA (for consistency with data.frame).

    o Fix bug in compare() (was not returning 0 when comparing a 0-width range
      to itself).

    o Fix naming of column when passing an AsIs matrix to DataFrame() -- no
      more .X suffix.

    o Fix "rbind" method for DataFrame objects when some columns are matrix
      objects.


CHANGES IN VERSION 1.16.0
-------------------------

NEW FEATURES

    o as( , "SimpleList"), as( , "CompressedList"), and as( , "List") now
      work on atomic vectors, and each element of the vector corresponds to
      an element of the returned List (this is consistent with as.list).

    o Add as.list,Rle method.

    o Add as.matrix,Views method. Each view corresponds to a row in the
      returned matrix. Rows corresponding to views shorter than the longest
      view are right-padded with NAs.

    o Add FilterClosure closure class for functions placed into a
      FilterRules. Has methods for getting parameters and showing.

    o Support 'na.rm' argument in "runsum", "runwtsum", "runq", and "runmean"
      methods for Rle and RleList objects.

    o Add splitAsList() and splitAsListReturnedClass().

    o Improve summary,FilterRules to support serial evaluation, discarded
      counts (instead of passed) and percentages.

    o Make rename work on ordinary vector (in addition to Vector).

    o Add coercion from RangedData to CompressedIRangesList, IRangesList, or
      RangesList. It propagates the data columns (aka values) of the RangedData
      object to the inner metadata columns of the RangesList object.

    o Add 'NG' arg to PartitioningByEnd() and PartitioningByWidth()
      constructors.

    o Make PartitioningByEnd() work on list-like objects (like
      PartitioningByWidth()).

    o Fast disjoin() for moderate-sized CompressedIRangesList.

    o Add countQueryHits() and countSubjectHits().

    o coverage() now supports method="auto" and this is the new default.

    o Add the flippedQuery(), levels(), ngap(), Lngap(), Rngap(), Lencoding(),
      and Rencoding() getters for OverlapEncodings objects.

    o Add "encodeOverlaps" method for GRangesList objects.

    o Enhance "[" methods for IRanges, XVector, XVectorList, and MaskCollection
      objects, as well as "[<-" method for IRanges objects, by supporting the
      following subscript types: NULL, Rle, numeric, logical, character, and
      factor. (All the methods listed above already supported some of those
      types but no method supported them all).

    o Add remapHits() for remapping the query and subject hits of a Hits
      object.

    o Add match,Hits method.

    o Add %in%,Vector method.

    o Add "compare", "==", "!=", "<=", ">=", "<", ">", "is.unsorted", "order",
      "rank", "match", and "duplicated" methods for XRawList objects. unique()
      and sort() also work on these objects via the "unique" and "sort" methods
      for Vector objects.

    o Add expand() for expanding a DataFrame based on the contents of one or
      more designated columms.

    o After being deprecated (in BioC 2.9) and defunct (in BioC 2.10), the
      "as.vector" method for AtomicList objects is back, but now it mimics
      what as.vector() does on an ordinary list i.e. it's equivalent to
      'as.vector(as.list(x), mode=mode)'. Also coercions from AtomicList to
      logical/integer/numeric/double/complex/character/raw are back and based
      on the "as.vector" method for AtomicList objects i.e. they work only on
      objects with top-level elements of length <= 1.

    o DataFrame constructor now supports 'check.names' argument.

    o Add revElements() generic with methods for List and CompressedList
      objects.

SIGNIFICANT USER-VISIBLE CHANGES
 
    o Splitting / relisting a Hits object now returns a HitsList instead of
      an ordinary list.

    o Operations in the Ops group between a List and an atomic vector operand
      now coerce the atomic vector to List (SimpleList or CompressedList)
      before performing the operation. Also, operands are recycled and a better
      job is done returning zero length results of the correct type.

    o Change the warning for 'Integer overflow ...' thrown by sum() on
      integer-Rle's

    o DataFrame now coerces List/list value to DataFrame in [<-.

    o Fix as.matrix,DataFrame for zero column DataFrames. Returns an nrow()x0
      logical matrix.

    o union,Hits method now sorts the returned hits first by query hit, then
      by subject hit.

    o Add mcols() accessor as the preferred way (over elementMetadata() and
      values()) to access the metadata columns of a Vector object.

    o By default, mcols(x) and elementMetadata(x) do NOT propagate the names
      of x as the row names of the returned DataTable anymore. However the
      user can still get the old behavior by doing mcols(x, use.names=TRUE).

    o [<-,XVectorList now preserves the original names instead of propagating
      the names of the replacement value, which is consistent with how [<-
      operates on an ordinary vector/list.

    o coverage() now returns a numeric-Rle when passed numeric weights.

    o When called on a List object with use.names=TRUE, unlist() no longer
      tries to mimic the kind of non-sense name mangling that base::unlist()
      does (e.g. on list(a=1:3)) in a pointless effort to return a vector
      with unique names.

    o Remove 'hits' argument from signature of encodeOverlaps() generic
      function.

    o unique,Vector now drops the names for consistency with base::unique().

    o Remove make.names() coercion in colnames<-,DataFrame for consistency
      with data.frame.

DEPRECATED AND DEFUNCT

    o Deprecated tofactor().

    o Remove RangesMatching, RangesMatchingList, and Binning classes.

    o Change from deprecated to defunct: matchMatrix(), "dim" method for Hits
      objects, and RangesMatchingList().

BUG FIXES

    o Fix bug in pintersect,IRanges,IRanges when input had empty ranges
      (broken since 2010-03-04).

    o Avoid integer overflow in mean,Rle method by coercing integer-Rle
      to numeric-Rle internally.

    o Change evaluation frame of with,List to parent.frame(), and get the
      enclosure correct in eval,List.

    o Many fixes and improvements to coercion from RangesList to RangedData
      (see commit 68195 for the details).

    o Fix "runValue" and "ranges" methods for CompressedRleList objects
      (broken for a very long time).

    o shift,Ranges method now fails in case of integer overflow instead of
      returning an invalid Ranges object.

    o mstack() now works on Vector objects with NULL metadata columns.

    o In case of integer overflow, coverage() now puts NAs in the returned
      Rle and issues a warning.

    o Fix bug in xvcopy,XRawList objects that prevented sequences from being
      removed from the cache of a BSgenome object. See commit 67171 for the
      details.

    o Fix issues related to duplicate column names in DataFrame (see commit
      67163 for the details).

    o Fix a bunch of subsetting methods that were not subsetting the metadata
      columns: "[", "subseq", and "seqselect" methods for XVector objects,
      "seqselect" and "window" methods for XVectorList objects, and "[" method
      for MaskCollection objects.         

    o Fix empty replacement with [<-,Vector

    o Make %in% robust on an empty 'table' argument when operating on Hits
      objects.


CHANGES IN VERSION 1.14.0
-------------------------

NEW FEATURES

    o The map generic and RangesMapping class for mapping ranges
      between sequences according to some alignment. Some useful
      methods are implemented in GenomicRanges.

    o The Hits class has experimental support for basic set
      operations, including setdiff, union and intersect.

    o Added a number of data manipulation functions and methods,
      including mstack, multisplit, rename, unsplit for Vector.

    o Added compare() generic for generalized range-wise comparison of 2
      range-based objects.

    o Added OverlapEncodings class and encodeOverlaps() generic for dealing
      with "overlap encodings".

    o subsetByOverlaps() should now work again on an RleViews object.

    o DataFrame now supports storing an array (like a matrix) in a column.

    o Added as.matrix,DataFrame method.

    o Added merge,DataTable,DataTable method.

    o Added disjointBins,RangesList method.

    o Added ranges,Rle and ranges,RleList methods.

    o Added which.max,Rle method.

    o Added drop,AtomicList method.

    o Added tofactor() wrapper around togroup().

    o Added coercions from vector to any AtomicList subtype (compressed and
      uncompressed).

    o Added AtomicList to Character/Numeric/Logical/Integer/Raw/ComplexList
      coercions.

    o Added revElements() for reversing individual elements of a List object.

SIGNIFICANT USER-VISIBLE CHANGES

    o RangesMatching has been renamed to Hits and extends Vector, so
      that it supports metadata columns and other features. 

    o RangesMatchingList has been renamed to HitsList.

    o The 2 columns of the matrix returned by the "as.matrix" method for Hits
      objects are now named queryHits/subjectHits instead of query/subject, for
      consistency with the queryHits() and subjectHits() getters.

    o queryLength()/subjectLength() are recommended alternatives to dim,Hits.

    o breakInChunks() returns a PartitioningByWidth object.

    o The 'weight' arg in "coverage" methods for IRanges, Views and
      MaskCollection objects now can also be a single string naming a column
      in elementMetadata(x).

    o "countOverlaps" methods now propagate the names of the query.

DEPRECATED AND DEFUNCT

    o matchMatrix,Hits is deprecated.

    o Moved the following deprecated features to defunct status:
      - use of as.data.frame() or as( , "data.frame") on an AtomicList object;
      - all coercion methods from AtomicList to atomic vectors;
      - subsetting an IRanges by Ranges;
      - subsetting a RangesList or RangedData by RangesList.

BUG FIXES

    o within,RangedData/List now support replacing columns

    o aggregate() override no longer breaks on . ~ x formulas

    o "[", "c", "rep.int" and "seqselect" methods for Rle objects are now
      safer and will raise an error if the object to be returned has a
      length > .Machine$integer.max 

    o Avoid blowing up memory by not expanding 'logical' Rle's into logical
      vectors internally in "slice" method for RleList objects.


CHANGES IN VERSION 1.12.0
-------------------------

NEW FEATURES

    o Add "relist" method that works on a List skeleton.

    o Add XDoubleViews class with support of most of the functionalities
      available for XIntegerViews.

    o c() now works on XInteger and XDouble objects (in addition to XRaw
      objects).

    o Add min, max, mean, sum, which.min, which.max methods as synonyms for
      the view* functions.

SIGNIFICANT USER-VISIBLE CHANGES

    o Views and RleViewsList classes don't derive from IRanges and IRangesList
      classes anymore.

    o When used on a List or a list, togroup() now returns an integer vector
      (instead of a factor) for consistency with what it does on other
      objects (e.g. on a Partitioning object).

    o Move compact() generic from Biostrings to IRanges.

    o Drop deprecated 'multiple' argument from "findOverlaps" methods.

    o Drop deprecated 'start' and 'symmetric' arguments from "resize" method
      for Ranges objects.

DEPRECATED AND DEFUNCT

   o Using as.data.frame() and or as( , "data.frame") on an AtomicList
     object is deprecated.

   o Deprecate all coercion methods from AtomicList to atomic vectors.
     Those methods were unlisting the object, which can still be done with
     unlist().

   o Deprecate the Binning class.

   o Remove defunct overlap() and countOverlap().

BUG FIXES

   o togroup() on a List or a list does not look at the names anymore to infer
     the grouping, only at the shape of the list-like object.

   o Fix 'relist(IRanges(), IRangesList())'.

   o Fix 'rep.int(Rle(), integer(0))'.

   o Fix some long-standing issues with the XIntegerViews code (better
     handling of "out of limits" or empty views, overflows, NAs).