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,
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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