SeqWare/queryengine — pull request #5 by denis-yuen (2013-10-04 19:41:45+00:00)
Title: Feature/plugin interface refactor

Refactor plugin interface so that plugins can be initialized with either a reference or a set of FeatureSets as a target (as opposed to one feature set). Add support for feature set tagging into the query language and add a plugin runner with filter support on the command line.
Also, some refactoring, fixing of maven targets, clean-up of inherited seqware commons classes.