CHANGES IN VERSION 1.15.3 -------------------------- o genome intervals order now consisten with assumption that (start == [start-1 and that stop) == stop-1] CHANGES IN VERSION 1.15.2 -------------------------- o Depends on intervals >=0.14.0 to fix a change in R's split behavior o sort does not have byName argument any longer NEW FEATURES o order, sort, rank and xtfrm consistently implemented. CHANGES IN VERSION 1.15.1 -------------------------- o Created that NEWS file to replace the CHANGES file and be compliant to the R standard package architecture NEW FEATURES o introduced a coercion to data.frame o introduced a writeGff3 function o reverted the sort behavior to the default R behavior and added a method argument. Setting it to byName results in a more biologically relevant sorting of the object. CHANGES IN VERSION 1.13.4 -------------------------- NEW FEATURES o annotation and annotation<- now from BiocGenerics. Thanks to Nicolas Delhomme. BUG FIXES o in interval_union use full argument name (levels instead of level) CHANGES IN VERSION 1.13.4 -------------------------- o updated Julien's email address CHANGES IN VERSION 1.13.4 -------------------------- NEW FEATURES o added a 'which_nearest' method for Genome_intervals objects CHANGES IN VERSION 1.11.1 -------------------------- NEW FEATURES o strand and strand<- now from BiocGenerics. Thanks to Nicolas Delhomme. CHANGES IN VERSION 1.7.5 -------------------------- NEW FEATURES o show only show the 1st 4 rows and the last 4 rows of a genomeIntervals CHANGES IN VERSION 1.7.4 -------------------------- NEW FEATURES o Added a 'sort' method for 'Genome_intervals' objects CHANGES IN VERSION 1.7.3 -------------------------- NEW FEATURES o Added a new user-friendly constructor function 'GenomeIntervals' for constructing both 'Genome_intervals' and 'Genome_intervals_stranded' objects CHANGES IN VERSION 1.7.2 -------------------------- BUG FIXES o regular expression in the extract method (called by parseGffAttributes()) fixed to make sure any key is at the beginning of after a ';' CHANGES IN VERSION 1.7.1 -------------------------- BUG FIXES o The package does not "Depends" on Biobase but only "Imports" it. o readGff3 deals with Gff having only "+" strand entries (bug report from Nicolas Servant) as well as "?" strand entries