Libraries

Third-party Components

Bamformatics uses a number of third-party libraries and add-ons (in alphabetical order):

• commons-compress 1.4 - library for IO with compressed files. Licenced under an Apache Licence
• Fugue icons - Some icons by Yusuke Kamiyamane. Licensed under a Creative Commons Attribution 3.0 License
• joptsimple 4.1 - command line option parsing. Licences under an MIT Licence
• jSeqUtils - library with miscellaneous tools for analysis of sequence data in java. Licenced under an Apache Licence
• sam-1.62 - library for manipulating alignment files, part of Picard package. Licences under an Apache Licence and an MIT Licence

Devlopment under:

• Netbeans 7.x - integrated development environment