CHANGES IN VERSION 1.4.7
------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Columns used for the filtering of results in the select call are automatically returned.
    o Ordering of results from select calls matches ordering of the provided keys (or of the
      values of a filter if only one was submitted).


CHANGES IN VERSION 1.4.6
-------------------------

BUG FIXES
    o Fix bug in ensDbFromGRanges if organism is whitespace-separated.


CHANGES IN VERSION 1.4.5
-------------------------

MINOR CHANGES
    o Fix typos in documentation.


CHANGES IN VERSION 1.4.4
-------------------------

BUG FIXES
    o Fix warning in BasicFilter validation.


CHANGES IN VERSION 1.4.3
-------------------------

BUG FIXES
    o tx_id was removed from metadata columns in txBy.
    o Fixed a bug that caused exon_idx column to be character if database created
      from a GTF.


CHANGES IN VERSION 1.3.20
-------------------------

BUG FIXES
    o methods transcripts, genes etc don't result in an error when columns are specified which
      are not present in the database and the return.type is GRanges.
    o Removed the transcriptLengths method implemented in ensembldb in favor of using the one
      from GenomicFeatures.


CHANGES IN VERSION 1.3.19
-------------------------

BUG FIXES
    o ensDbFromGRanges (and thus ensDbFromGtf, ensDbFromGff and ensDbFromAH) support now
      Ensembl GTF file formats from version 74 and before.


CHANGES IN VERSION 1.3.18
-------------------------

NEW FEATURES
    o New ExonrankFilter to filter based on exon index/rank.


CHANGES IN VERSION 1.3.17
-------------------------

BUG FIXES
    o Use setdiff/intersect instead of psetdiff/pintersect.


CHANGES IN VERSION 1.3.16
-------------------------

BUG FIXES
    o Fixed failing test.


CHANGES IN VERSION 1.3.15
-------------------------

NEW FEATURES
    o GRangesFilter now supports GRanges of length > 1.
    o seqlevels method for GRangesFilter.
    o New methods exonsByOverlaps and transcriptsByOverlaps.


CHANGES IN VERSION 1.3.14
-------------------------

NEW FEATURES
    o seqlevelsStyle getter and setter method to change the enable easier integration
      of EnsDb objects with UCSC based packages. supportedSeqlevelsStyle method to list
      possible values. Global option "ensembldb.seqnameNotFound" allows to adapt the
      behaviour of the mapping functions when a seqname can not be mapped properly.
    o Added a seqlevels method for EnsDb objects.

SIGNIFICANT USER-VISIBLE CHANGES
    o Add an example to extract transcript sequences directly from an EnsDb object to
      the vignette.
    o Add examples to use EnsDb objects with UCSC chromosome names to the vignette.

BUG FIXES
    o Seqinfo for genes, transcripts and exons contain now only the seqnames returned
      in the GRanges, not all that are in the database.


CHANGES IN VERSION 1.3.13
-------------------------

NEW FEATURES
    o EnsDb: new "hidden" slot to store additional properties and a method updateEnsDb
      to update objects to the new implementation.
    o New method "transcriptLengths" for EnsDb that creates a similar data.frame than
      the same named function in the GenomicFeatures package.

BUG FIXES
    o fiveUTRsByTranscript and threeUTRsByTranscript returned wrong UTRs for some special
      cases in which the CDS start and end were in the same exon. This has been fixed.


CHANGES IN VERSION 1.3.12
-------------------------

NEW FEATURES
    o ensDbFromGff and ensDbFromAH functions to build EnsDb objects from GFF3 files
      or directly from AnnotationHub ressources.
    o getGenomeFaFile does now also retrieve Fasta files for the "closest" Ensembl
      release if none is available for the matching version.

SIGNIFICANT USER-VISIBLE CHANGES
    o Removed argument 'verbose' in ensDbFromGRanges and ensDbFromGtf.
    o Updated parts of the vignette.
    o Removed method extractTranscriptSeqs again due to some compatibility problems
      with GenomicRanges.

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 1.3.11
-------------------------

BUG FIXES
    o "select" method returns now also the keytype as a column from the database.


CHANGES IN VERSION 1.3.10
-------------------------

NEW FEATURES
    o Implemented methods columns, keys, keytypes, mapIds and select from AnnotationDbi.
    o Methods condition<- and value<- for BasicFilter.


CHANGES IN VERSION 1.3.9
------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o The shiny app now allows to return the search results.



CHANGES IN VERSION 1.3.7
------------------------

SIGNIFICANT USER-VISIBLE CHANGES
    o Some small changes to the vignette.

BUG FIXES
    o Fixed a problem in an unit test.


CHANGES IN VERSION 1.3.6
------------------------

BUG FIXES
    o Fixed a bug in ensDbFromGRanges.


CHANGES IN VERSION 1.3.5
------------------------

NEW FEATURES
    o Added GRangesFilter enabling filtering using a (single!) GRanges object.
    o Better usability and compatibility with chromosome names: SeqnameFilter and
      GRangesFilter support both Ensembl and UCSC chromosome names, if option
      ucscChromosomeNames is set to TRUE returned chromosome/seqnames are in
      UCSC format.

SIGNIFICANT USER-VISIBLE CHANGES
    o Added method "value" for BasicFilter objects.

BUG FIXES
    o transcripts, genes, exons return now results sorted
      by seq name and start coordinate.


CHANGES IN VERSION 1.3.4
------------------------

NEW FEATURES
    o Added extractTranscriptSeqs method for EnsDb objects.


SIGNIFICANT USER-VISIBLE CHANGES
    o Added a section to the vignette describing the use of ensembldb in Gviz.
    o Fixed the vignette to conform the "Bioconductor style".
    o Added argument use.names to exonsBy.

BUG FIXES
    o Fixed bug with getGeneRegionTrackForGviz with only chromosome specified.
    o Fixed an internal problem subsetting a seqinfo.


CHANGES IN VERSION 1.3.3
------------------------

NEW FEATURES
    o Add method getGeneRegionTrackForGviz to enable using EnsDb databases for Gviz.

BUG FIXES
    o cdsBy, fiveUTRsForTranscript and threeUTRsForTranscript do no longer throw
      an error if nothing was found but return NULL and produce a warning.



CHANGES IN VERSION 1.3.2
------------------------

NEW FEATURES
    o Implemented methods cdsBy, fiveUTRsForTranscript and threeUTRsForTranscript
      for EnsDb.



CHANGES IN VERSION 1.3.1
------------------------

BUG FIXES
    o Ensuring that methods exons, genes and transcripts return columns in the
      same order than provided with argument 'columns' for return.type 'data.frame'
      or 'DataFrame'.



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".


