David Roazen 1213b2f8c6 SnpEff 2.0.2 support ... -Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2) -Removed support for SnpEff 1.9.6 (and associated tribble codec) -Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag) -Correctly matches ref/alt alleles before annotating a record, unlike the previous version -Correctly handles indels (again, unlike the previous version		2011-09-14 07:09:47 -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	SnpEff 2.0.2 support	2011-09-14 07:09:47 -04:00
packages	Removing some old cruft from the packages dir. Updating AnalyzeCovariates to include all Covariates.	2011-09-12 15:09:25 -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