=============
Release Notes
=============

The code collection is under continuous improvement and the 
latest code can always be found in the code repository.
Nevertheless, we occasionally prepare releases. Notes on
each release are below.

Release 0.2
===========

* release for CGAT manuscript - fixed various installation issues

Release 0.1.9
=============

* alignlib incompatibility fixed
* various bugfixes

Release 0.1.8
=============

* OS X compatibility release
* various bugfixes

Contributors
============

The following people have contributed to the CGAT Code collection:

* Andreas Heger
* Antonio Berlanga-Taylor
* Martin Dienstbier
* Nicholas Ilott
* Jethro Johnson
* Katherine Fawcett
* Stephen Sansom
* David Sims
* Ian Sudbery
* Hu Xiaoming
* Lesheng Kong

3rd party code
==============

The CGAT code collection has been made possible by the many developers
in the bioinformatics and python community that have made their code
available for sharing. The code collection includes some snippets of
code taken from elsewhere for convenience, most notably:

1. IGV.py from Brent Petersen 
   https://github.com/brentp/bio-playground/blob/master/igv/igv.py

2. Nested containment list from the Pygr project
   http://code.google.com/p/pygr/

3. SVGdraw.py was written by Fedor Baart & Hans de Wit

4. list_overlap.py from Brent Petersen
   https://github.com/brentp/bio-playground/blob/master/utils/list_overlap_p.py

5. Iterators.py from an unknown source.

Licence
=======

The CGAT code is released under the new BSD licence::

    Copyright (c) 2013, Andreas Heger, MRC CGAT

    All rights reserved.

    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:

	Redistributions of source code must retain the above copyright
	notice, this list of conditions and the following disclaimer.
	Redistributions in binary form must reproduce the above copyright
	notice, this list of conditions and the following disclaimer in
	the documentation and/or other materials provided with the
	distribution.  Neither the name of the Medical Research Council nor the
	names of its contributors may be used to endorse or promote
	products derived from this software without specific prior written
	permission.

    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
    HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
    LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
    DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.