NEWS

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genomeIntervals 1.45.2

• Ported changes from 1.44.2

genomeIntervals 1.45.1

• Ported changes from 1.44.1

genomeIntervals 1.44.2

• Updated the maintainer email address
• Cleared the imports

genomeIntervals 1.44.1

• Updated the vignette (data.frame() default is not a factor anymore for character vectors in R4)
• Removed the defunct RangedData usage

genomeIntervals 1.31.1

• the signature of rank() has now ... and "last" as option in ties.method (for compatibility only -- not supported)

genomeIntervals 1.25.3

• Changed the "c" function from an S3method to use the S4 generic.

genomeIntervals 1.25.2

• Fixed the width function to handle correctly the left end of the intervals

genomeIntervals 1.25.1

• 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)
• Deprecated the seq_name accessors in favour of the BiocGenerics seqnames
• Added a width accessor - similar to the IRanges functionality
• Added coercion to GRangesList and RangedData
• Edited some of the documentation (man page) and NAMESPACE generation to use roxygen2

genomeIntervals 1.25.0

• Bioc Version 3.2 devel

genomeIntervals 1.24.1

• Fixing Git-SVN issues

genomeIntervals 1.24.0

• Bioc Version 3.1 release

genomeIntervals 1.23.2

• Ported version 1.22.2-1.22.3 changes

genomeIntervals 1.23.1

• Ported version 1.22.1 changes

genomeIntervals 1.23.0

• Bioc Version 3.1

genomeIntervals 1.22.3

• Fixed a documentation cosmetic issue

genomeIntervals 1.22.2

• Fixed a pretty printing issue if the formatting (inclusion of space)

genomeIntervals 1.22.1

• Fixed an issue in the formatting of the coordinates in the writeGff3 function

genomeIntervals 1.22.0

• Bioc Version 3.0

genomeIntervals 1.21.1

• Ported version 1.20.1 changes

genomeIntervals 1.20.1

• Added an argument to the readGff3 function to enable quietness.
• Corrected some R CMD check warnings

genomeIntervals 1.15.3

• genome intervals order now consisten with assumption that (start == [start-1 and that stop) == stop-1]

genomeIntervals 1.15.2

• Depends on intervals >=0.14.0 to fix a change in R's split behavior
• sort does not have byName argument any longer NEW FEATURES
• order, sort, rank and xtfrm consistently implemented.

genomeIntervals 1.15.1

• Created that NEWS file to replace the CHANGES file and be compliant to the R standard package architecture NEW FEATURES
• introduced a coercion to data.frame
• introduced a writeGff3 function
• 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.

genomeIntervals 1.13.4

• annotation and annotation<- now from BiocGenerics. Thanks to Nicolas Delhomme.
• in interval_union use full argument name (levels instead of level)
• updated Julien's email address
• added a 'which_nearest' method for Genome_intervals objects

genomeIntervals 1.11.1

NEW FEATURES

• strand and strand<- now from BiocGenerics. Thanks to Nicolas Delhomme.

genomeIntervals 1.7.5

NEW FEATURES

• show only show the 1st 4 rows and the last 4 rows of a genomeIntervals

genomeIntervals 1.7.4

NEW FEATURES

• Added a 'sort' method for 'Genome_intervals' objects

genomeIntervals 1.7.3

NEW FEATURES

• Added a new user-friendly constructor function 'GenomeIntervals' for constructing both 'Genome_intervals' and 'Genome_intervals_stranded' objects

genomeIntervals 1.7.2

BUG FIXES

• regular expression in the extract method (called by parseGffAttributes()) fixed to make sure any key is at the beginning of after a ';'

genomeIntervals 1.7.1

BUG FIXES

• The package does not "Depends" on Biobase but only "Imports" it.
• readGff3 deals with Gff having only "+" strand entries (bug report from Nicolas Servant) as well as "?" strand entries