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).