CHANGES IN VERSION 1.7.0
-------------------------

NEW FEATURES

    o geneModel, geneList classes added


SIGNIFICANT USER-VISIBLE CHANGES

    o (none)

BUG FIXES

    o (none)


CHANGES IN VERSION 1.6.0
-------------------------

NEW FEATURES

    o getSpliceTable additionally copies transcript_biotype when present

    o unifyJuncs counts number of transcripts which are classified as
        nonsense mediated decay

    o unifyJuncs now returns refJunctions (i.e. same class as passed object)

    o Added extractByGeneId function


SIGNIFICANT USER-VISIBLE CHANGES

    o (none)

BUG FIXES

    o (none)


CHANGES IN VERSION 1.5.0
-------------------------

NEW FEATURES

    o (none)

SIGNIFICANT USER-VISIBLE CHANGES

    o New C++ based import of GTF files due to import errors in Ensembl 76 (1.4.2). The attributes table and
	related functions are removed.

BUG FIXES

    o The new GTF import mechanism is included because the former version produced an error.


CHANGES IN VERSION 1.4.0
-------------------------

NEW FEATURES

    o Added a 'unifiedExons' class and 

    o Change compilation of source code to C++11 (from C)


SIGNIFICANT USER-VISIBLE CHANGES

    o Added support for unification of exonic sites which can be used for counting alignments (reads)

BUG FIXES

    o (none)


CHANGES IN VERSION 1.2.8
-------------------------

NEW FEATURES

    o Included this NEWS file and a ChangeLog file

    o Added a unifyJuncs method: A method for unification of splice sites

    o Added overlapJuncs functions: A specialized routine for annotation of splice junctions


SIGNIFICANT USER-VISIBLE CHANGES

    o Added support for 'gene' records in gtf file (as introduced by Ensembl 76)

BUG FIXES

    o (none)
