Before use, untar seqdir.tgz and virtdir.tgz.  This is the test data.

To check the function of RagbagDirectoryHandler on concrete sequences:-
java TestRagbagAssembly seqdir

This will instantiate an in-memory object where annotations in Annotation/ are applied to 
seqdir/AE003462.2.game.

To test the function of RagbagDirectoryHandler on virtual sequences:-
java TestRagbagAssembly virtdir

This will construct a virtual sequence (SimpleAssembly) onto which the three sequences 
comprising the left tip of the Drosophila X-chromosome are mapped. The format of 
the Map file can be seen in virtdir/Map.  Basically, it's an XML format.

Enjoy,
David Huen, Dept. of Genetics, Univ. of Cambridge