altSpliceFinder Release Notes - User visible changes.

Release 0.5.3 (28 January 2011)
-------------------------------

* Use boost library release 1.45.0 to parse options
 
Release 0.5.2 (03 February 2010)
--------------------------------

* First distribution as part of Ensembl

Release 0.5.1 (15 January 2010)
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* Corrected options to compute statistics (--statistiscs|-s)
  Released by Gautier Koscielny, based on stable version 0.5.

Release 0.5 (08 December 2009)
------------------------------

* Major changes in altSpliceFinder 0.5 [stable]
  Released by Gautier Koscielny, based on stable version 0.4.

** relax mode: option ``-relax|-r'' to compute cassette exons and mutually
   exclusive events with relaxed constraints on flanking exons.
   In this mode, flanking exons are required to overlap but the constraints 
   on the same 3p or 5p end is removed.

** bug on A5SS computation fixed.

** remove spurious STDERR logs on intron retention event 
   computations.

Release 0.4 (13 May 2009)
-------------------------

* Major changes in altSpliceFinder 0.4 (2009-05-13) [stable]
  Released by Gautier Koscielny, based on stable version 0.3.

** GFF output: each feature in featuresA or featuresB is followed by a list 
   of corresponding transcripts in brackets.

** constitutive mode: option ``-constitutives|-c'' to compute constitutive exons 
   events only.

** bug on constitutive exon computation fixed.

Release 0.3 (27 January 2009)
-----------------------------

* Major changes in altSpliceFinder 0.3 (2009-01-27) [stable]
  Released by Gautier Koscielny, based on stable version 0.2.

** Unique ID for each event based on gene ID and event type: 
   <gene_id>-<event_type>-number

** Splice sites coordinates added for each feature of each type of events.

** Extension of Intron Retention computations to catch more cases (not only 
   exact exon 5p/3p but also overlapping cases).

** Log4C++ Verbose mode added.

** GNU Configure program with Log4CPP libraries dependencies.

Release 0.2 (13 January 2009)
-----------------------------

* Major changes in altSpliceFinder 0.2 (2009-01-13) [stable]
  Released by Gautier Koscielny, based on stable version 0.1.

** Alternative First Exon (AFE) event computation.

** Alternative Last Exon (ALE) event computation.

** Constitutive Exon (CNE) event computation module added.

** Source code directory structure reflects C++ namespace structure.

** Replace the traditional Makefile with a GNU Configure program
   including Boost libraries dependencies.

** GPL license added.

release 0.1 (December 2008)
---------------------------

* First release by Gautier Koscielny

** Cassette Exon (CE)  event computation.

** Intron Isoform (II) event computation.

** Exon Isoform (EI) event computation.

** Intron Retention (IR) event computation.

** Mutually Exclusive (MXE) event computation.

** Alternative Initiation (AI) event computation.

** Alternative Termination (AT) event computation.

** Simple makefile.

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but WITHOUT ANY WARRANTY; without even the implied warranty of
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