https://sourceforge.net/p/geneticthesaurus/wiki/Development/Recent changes to DevelopmentenWed, 14 Jan 2015 16:52:39 -0000https://sourceforge.net/p/geneticthesaurus/wiki/Development/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -3,7 +3,7 @@ ####Source code### -Version 0.1.0 is available in java bytecode form only. Open source code will be available at github.com upon academic publication. +Open source code is available at [github.com](https://github.com/) in repository [GeneticThesaurus](https://github.com/tkonopka/GeneticThesaurus). ####Third-party libraries#### </pre> </div>TomaszWed, 14 Jan 2015 16:52:39 -0000https://sourceforge.neta60d3f7cdafd7a264b125f5c21a13d3c6df1418dhttps://sourceforge.net/p/geneticthesaurus/wiki/Development/<div class="markdown_content"><h2 id="development">Development</h2> <h4 id="source-code">Source code</h4> <p>Version 0.1.0 is available in java bytecode form only. Open source code will be available at github.com upon academic publication.</p> <h4 id="third-party-libraries">Third-party libraries</h4> <p>GeneticThesaurus relies on some third-party libraries.</p> <ul> <li><a class="" href="http://pholser.github.com/jopt-simple/" rel="nofollow">joptsimple 4.1</a> - command line option parsing. Licenced under an <a class="" href="http://opensource.org/licenses/mit-license.phphttp://opensource.org/licenses/mit-license.php" rel="nofollow">MIT Licence</a></li> <li><a class="" href="http://commons.apache.org/compress/" rel="nofollow">commons-compress 1.4</a> - library for reading and writing compressed files. Licenced under an <a class="" href="http://www.apache.org/licenses/http://www.apache.org/licenses/" rel="nofollow">Apache Licence</a></li> <li><a class="" href="https://sourceforge.net/projects/picard/https://sourceforge.net/projects/picard/">sam-1.62</a> - library for manipulating alignment files, part of Picard package. Licenced under an <a class="" href="http://www.apache.org/licenses/http://www.apache.org/licenses/" rel="nofollow">Apache Licence</a> and an <a class="" href="http://opensource.org/licenses/mit-license.phphttp://opensource.org/licenses/mit-license.php" rel="nofollow">MIT Licence</a></li> </ul> <p>Source code is developed locally under the <a class="" href="http://netbeans.org/" rel="nofollow">Netbeans</a> integrated development environment.</p> <h4 id="testing">Testing</h4> <p>GeneticThesaurus should function on all platforms where java is available and should be compatible with most datasets (bam files and variants call files). However, testing was primarily performed on a linux system using alignments produced by Bowtie2 and variant call files produced by Bamformatics.</p></div>TomaszSat, 03 May 2014 07:00:09 -0000https://sourceforge.net41df355991286b5c72f7c26ea8691737b158f612