5 Commits (77ef2be9b8738f8bf8ee5455fece59647b1b20b1)

Author	SHA1	Message	Date
Khalid Shakir	b090751f62	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths. ... Updates to HybridSelectionPipeline: - Added annotations back via snpEff - Minor updates to VQSR paths and lowered memory	2011-09-27 14:33:57 -04:00
Mark DePristo	f7414e39bc	Improvements to GATKDocs ... -- Allowed values for RodBinding<T> are displayed in the GATKDocs -- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio) -- Features are listed in alphabetical order -- Moved useful getParameterizedType() function to JVMUtils -- Tests of these features in the Documentation Test	2011-08-18 21:20:09 -04:00
Mark DePristo	e36994e36b	Refactored a FeatureManager class from RMDTrackBuilder ... New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK. Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.	2011-08-08 14:04:46 -04:00
Mark DePristo	9992c373be	Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes.	2011-07-17 20:29:58 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00