David Roazen 9d9d438bc4 New VariantAnnotatorEngine capability: an initialize() method for all annotation classes. ... All VariantAnnotator annotation classes may now have an (optional) initialize() method that gets called by the VariantAnnotatorEngine ONCE before annotation starts. As an example of how this can be used, the SnpEff annotation class will use the initialize() method to check whether the SnpEff version number stored in the vcf header is a supported version, and also to verify that its required RodBinding is present.		2011-09-12 13:00:53 -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	New VariantAnnotatorEngine capability: an initialize() method for all annotation classes.	2011-09-12 13:00:53 -04:00
packages	Added edu.mit.broad.picard to Queue packaged jar.	2011-07-23 14:40:29 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00