David Roazen 0d163e3f52 SnpEff 2.0.4 support ... -Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format -Assigning functional classes and effect impacts now handled directly by SnpEff rather than the GATK -Removed support for SnpEff 2.0.2, as we no longer trust the output of that version since it doesn't exclude effects associated with certain nonsensical transcripts. These effects are excluded as of 2.0.4. -Updated unit and integration tests This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject to change between now and the next GATK release.		2011-11-15 18:36:22 -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	SnpEff 2.0.4 support	2011-11-15 18:36:22 -05:00
jna	Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE	2011-09-23 21:03:22 -04:00
pipeline	Cleanup of the utils.broad package.	2011-07-01 20:47:03 -04:00
utils	The right fix for this test is just to delete it.	2011-11-15 14:53:27 -05:00
BaseTest.java	merge master	2011-10-25 16:08:39 -04:00
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