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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R	Compacting pdfs when running under R 2.13+.	2011-10-27 14:51:56 -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	SnpEff 2.0.4 support	2011-11-15 18:36:22 -05:00
packages	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Don't generate PDF unless you have -run specified	2011-11-09 14:45:40 -05:00
testdata	Testdata for IntervalStratification	2011-11-10 11:08:34 -05:00