CHANGES IN VERSION 1.2.2
------------------------

BUG FIXES
    o Avoid wrong CDS start/end position definition for Ensembl gtf files in which the
      start or end codon is outside the CDS.



CHANGES IN VERSION 1.1.9
------------------------

BUG FIXES

    o Fixed a figure placement problem that can result in an error on certain
      systems using a recent TexLive distribution.



CHANGES IN VERSION 1.1.6
------------------------

BUG FIXES

    o Fix a bug in lengthOf that caused an error if no filter was supplied.


CHANGES IN VERSION 1.1.5
------------------------

NEW FEATURES

    o Implemented a shiny web app to search for genes/transcripts/exons using
      annotation of an EnsDb annotation package (function runEnsDbApp).



CHANGES IN VERSION 1.1.4
------------------------

NEW FEATURES

    o Added promoters method.



CHANGES IN VERSION 1.1.3
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added method ensemblVersion that returns the Ensembl version the package bases on.
    o Added method getGenomeFaFile that queries AnnotationHub to retrieve the Genome
      FaFile matching the Ensembl version of the EnsDb object.


CHANGES IN VERSION 1.1.2
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added examples to the vignette for building an EnsDb using AnnotationHub along with
      the matching genomic sequence.
    o Added an example for fetching the sequences of genes, transcripts and exons to the vignette.


BUG FIXES

    o Fixed a bug in ensDbFromGRanges and ensDbFromGtf in which the genome build version
      was not set even if provided.



CHANGES IN VERSION 1.1.1
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The filter argument in all functions supports now also submission of a filter
      object, not only of a list of filter objects.



CHANGES IN VERSION 0.99.18
--------------------------

BUG FIXES

    o Fixed a problem in processing GTF files without header information.

    o Fixed a bug failing to throw an error if not all required feature types are
      available in the GTF.



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

NEW FEATURES

    o Added new function ensDbFromGRanges that builds an EnsDB database from information
      provided in a GRanges object (e.g. retrieved from the AnnotationHub).



CHANGES IN VERSION 0.99.16
--------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added argument outfile to ensDbFromGtf that allows to manually specify the file
      name of the database file.

    o ensDbFromGtf tries now to automatically fetch the sequence lengths from Ensembl.


BUG FIXES

    o Fixed the function that extracts the genome build version from the gtf file name.



CHANGES IN VERSION 0.99.15
--------------------------

NEW FEATURES

    o metadata method to extract the information from the metadata database table.

    o ensDbFromGtf function to generate a EnsDb SQLite file from an (Ensembl)
      GTF file.



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

BUG FIXES

    o Fixed a problem when reading tables fetched from Ensembl that contained ' or #.



CHANGES IN VERSION 0.99.13
--------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added argument "port" to the fetchTablesFromEnsembl to allow specifying the MySQL port
      of the database.



CHANGES IN VERSION 0.99.12
--------------------------

BUG FIXES

    o argument "x" for method organism changed to "object".