CHANGES IN VERSION 1.14.0
-------------------------

NEW FEATURES

SIGNIFICANT USER-VISIBLE CHANGES

DEPRECATED AND DEFUNCT

    o Remove 'force' argument from seqinfo() and seqlevels() setters (the
      argument got deprecated in BioC 3.5 in favor of new and more flexible
      'pruning.mode' argument).

BUG FIXES

    o Add missing Y/chrY entry in seqlevel style db for Drosophila
      melanogaster and Rattus norvegicus.


CHANGES IN VERSION 1.12.0 
-------------------------

NEW FEATURES

    o Add function standardChromosomes()

    o Seqlevels() setter now supports "fine" and "tidy" modes on GRangesList and
    GAlignmentsList objects

    o Add assembly_accessions dataset

MODIFICATIONS

    o Updated mapping table between UCSC and Ensembl to include recent builds

    o Use https instead of http to fetch stuff from NCBI

    o Replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter

    o Add 'pruning.mode' argument to the keepSeqlevels(), dropSeqlevels(), and
    keepStandardChromosomes() functions. IMPORTANT NOTE: Like for the
    seqlevels() setter, the default pruning mode is "error", which means that
    now these functions fail when some of the seqlevels to drop from 'x' are in
    use. The old behavior was to silently prune 'x' (doing "coarse" pruning)

    o Update files in data directory 

    o Updated internal functions .lookup_refseq_assembly_accession() and
    fetch_assembly_report() for speed and efficiency 

    o move some files from GenomeInfoDb/data/ to GenomeInfoDbData annotation package

BUG FIXES

    o fetch_assembly_summary() updated to work with recent changes to format of
    files assembly_summary_genbank.txt and assembly_summary_refseq.txt

CHANGES IN VERSION 1.10.0 
------------------------------

NEW FEATURES

    o Add function mapGenomeBuilds() that maps between UCSC and Ensembl
    builds. 

    o Add function genomeBuilds() that list all the available UCSC or Ensembl
    builds for a given organism[s] that can be used in mapGenomeBuilds() 

    o Add listOrganism() that list all currently available organism[s] included
    for use in genomeBuilds()

DEPRECATED AND DEFUNCT

    o After being deprecated, the species() method for GenomeDescription objects
    is now defunct

MODIFICATIONS

    o Zebra finch is removed as option for
    fetchExtendedChromInfoFromUCSC() as it is not support yet

    o keepStandardChromosomes() chooses first style when multiple are matched

BUG FIXES

    o Fix WARNING occuring when determining style in keepStandardChromosomes() 


CHANGES IN VERSION 0.99.7
----------------------------------

MODIFICATIONS

   o rename:
     isSupportedSeqnames -> .isSupportedSeqnames
     supportedSeqnameStyles -> .supportedSeqnameStyles
     supportedSeqnameMappings -> .supportedSeqnameMappings
     isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle


CHANGES IN VERSION 0.99.6 
----------------------------------

NEW FEATURES

   o add new functions()
     seqnamesInGroup which will take a character vector of chromosomes and 
     return the chromosomes specified by the group parameter supplied by the 
     user. The user can also give the species and the style.
     seqnamesOrder() internally calls Herve's function makeSeqnameIds()
   o add seqnameStyles generic and method from GenomicRanges

MODIFICATIONS

   o rename:
     testSeqnames -> isSupportedSeqnames

   o move SeqnamesStyle generic from GenomicRanges and define a new method which
     works on a character vector.
         
DEPRECATED AND DEFUNCT

   o deprecate listAllSupportedStylesBySpecies(), 
     listAllSupportedSeqnameStyles(), supportedOrganisms()
     supportedSeqnameMappingsWithGroup()
       
   o deprecate supportedSeqnameMappings(), supportedSeqnameStyles(), 
     isSupportedSeqnamesStyle(),issupportedSeqnames()


CHANGES IN VERSION 0.99.17
----------------------------------

MODIFICATIONS

   o keepStandardChromosomes: Make 'species' argument optional and remove 
     'style' argument.


CHANGES IN VERSION 0.99.14
----------------------------------

MODIFICATIONS

   o rename:
     package: Seqnames --> GenomeInfoDb

     supportedStyles -> genomeStyles

     makeSeqnameIds --> rankSeqlevels   (add to export)
     seqnamesOrder --> orderSeqlevels

     extractSeqnameSet -> extractSeqlevels
     extractSeqnameSetByGroup -> extractSeqlevelsByGroup
     findSequenceRenamingMaps --> mapSeqlevels
     seqnamesInGroup --> seqlevelsInGroup
     seqnamesStyle --> seqlevelsStyle
     "seqnameStyle<-" --> "seqlevelsStyle<-" 


CHANGES IN VERSION 0.99.1
------------------------------

NEW FEATURES
 
   o added new functions:
     supportedOrganisms()  
     supportedSeqnameMappingsWithGroup()  
     extractSeqnameSetByGroup() 

MODIFICATIONS

    o The Seqnames package will have functions which will be moved from 
    AnnotationDbi , GenomicRanges

   o List of 9 functions moved from AnnotationDbi
     supportedSeqnameMappings, findSequenceRenamingMaps, 
     supportedSeqnameStyles,  supportedSeqnames, 
     extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle,
     listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles.
        
   o makeSeqnameIds moved from GenomicRanges
     
   o keepStandardChromosomes moved from GenomicRanges 
     
   o rename:
     keepStandardChromosomes -> keepChromosomes