Development

Development

Source code

Open source code is available at github.com in repository GeneticThesaurus.

Third-party libraries

GeneticThesaurus relies on some third-party libraries.

• joptsimple 4.1 - command line option parsing. Licenced under an MIT Licence
• commons-compress 1.4 - library for reading and writing compressed files. Licenced under an Apache Licence
• sam-1.62 - library for manipulating alignment files, part of Picard package. Licenced under an Apache Licence and an MIT Licence

Source code is developed locally under the Netbeans integrated development environment.

Testing

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.