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).