CHANGES IN VERSION 1.45.2 -------------------------- o Ported changes from 1.44.2 CHANGES IN VERSION 1.45.1 -------------------------- o Ported changes from 1.44.1 CHANGES IN VERSION 1.44.2 -------------------------- o Updated the maintainer email address o Cleared the imports CHANGES IN VERSION 1.44.1 -------------------------- o Updated the vignette (data.frame() default is not a factor anymore for character vectors in R4) o Removed the defunct RangedData usage CHANGES IN VERSION 1.31.1 -------------------------- o the signature of rank() has now ... and "last" as option in ties.method (for compatibility only -- not supported) CHANGES IN VERSION 1.25.3 -------------------------- o Changed the "c" function from an S3method to use the S4 generic. CHANGES IN VERSION 1.25.2 -------------------------- o Fixed the width function to handle correctly the left end of the intervals CHANGES IN VERSION 1.25.1 -------------------------- o Changed readGff3 to use closed intervals by default. Implemented two sub-functions that implement reading a gff3 as base-pair features only (no zero length intervals, i.e. right-closed intervals) or which allows for zero length intervals, i.e. right-open intervals, when start equals end) o Deprecated the seq_name accessors in favour of the BiocGenerics seqnames o Added a width accessor - similar to the IRanges functionality o Added coercion to GRangesList and RangedData o Edited some of the documentation (man page) and NAMESPACE generation to use roxygen2 CHANGES IN VERSION 1.25.0 -------------------------- o Bioc Version 3.2 devel CHANGES IN VERSION 1.24.1 -------------------------- o Fixing Git-SVN issues CHANGES IN VERSION 1.24.0 -------------------------- o Bioc Version 3.1 release CHANGES IN VERSION 1.23.2 -------------------------- o Ported version 1.22.2-1.22.3 changes CHANGES IN VERSION 1.23.1 -------------------------- o Ported version 1.22.1 changes CHANGES IN VERSION 1.23.0 -------------------------- o Bioc Version 3.1 CHANGES IN VERSION 1.22.3 -------------------------- o Fixed a documentation cosmetic issue CHANGES IN VERSION 1.22.2 -------------------------- o Fixed a pretty printing issue if the formatting (inclusion of space) CHANGES IN VERSION 1.22.1 -------------------------- o Fixed an issue in the formatting of the coordinates in the writeGff3 function CHANGES IN VERSION 1.22.0 -------------------------- o Bioc Version 3.0 CHANGES IN VERSION 1.21.1 -------------------------- o Ported version 1.20.1 changes CHANGES IN VERSION 1.20.1 -------------------------- o Added an argument to the readGff3 function to enable quietness. o Corrected some R CMD check warnings 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