Description of how Standalone AutoCSA can be integrated into a pipeline.

See:
          Description

Packages
uk.ac.sanger.cgp.standalonecsa.beans The beans used by Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.control The controlling main methods used in the application.
uk.ac.sanger.cgp.standalonecsa.enums The immutable objects used in Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.exceptions The exception classes used in Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.gui The interactive setup GUI used in the Standalone AutoCSA application.
uk.ac.sanger.cgp.standalonecsa.interfaces The service interface classes used in Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.jabawat The core of the alignment system used in Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.services The implementations of the services used in Standalone AutoCSA.
uk.ac.sanger.cgp.standalonecsa.util The utility classes used in Standalone AutoCSA.

 

Description of how Standalone AutoCSA can be integrated into a pipeline.

If you wish to use this package as part of your pipeline, but with more control of the processing, the following methods do the actual work and must be run in the following order:

This will give you the raw results from the analysis system.