David Roazen 506c0e9c97 Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline ... SnpEff support will remain disabled until SnpEff 2.0.4 has been officially released and we've verified the quality of its annotations.		2011-12-23 19:12:57 -05:00
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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Disabling SnpEff support in the GATK and SnpEff annotation in the HybridSelectionPipeline	2011-12-23 19:12:57 -05:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Updated IntegrationTests with new adaptor clipper	2011-12-20 17:48:52 -05:00
BaseTest.java	Removing cruft that snuck in last commit.	2011-12-16 23:00:16 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	All MD5 mismatches for test are shown	2011-10-04 15:53:52 -07:00