David Roazen 24b72334b3 UnifiedGenotyper now correctly initializes the VariantAnnotator engine. ... This allows the annotation classes to perform any necessary initialization/validation. For example, it allows the SnpEff annotator to (among other things) validate its rod binding. This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding is present. Added an integration test to cover this case so that it doesn't break again.		2011-10-11 12:02:05 -04:00
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R	Fixing units in queue job report Gantt plots	2011-09-12 09:01:34 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	UnifiedGenotyper now correctly initializes the VariantAnnotator engine.	2011-10-11 12:02:05 -04:00
packages	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00