Add the snpeff wrappers from Jim Johnson!
add missing files
special statsFile handling
add wrapper for "SnpSift.jar geneSets"
Enhance SnpEff readmes.
Select default for spliceSiteSize param. Add output label. Fix typos.
Fix a test param. Cosmetic fixes.
Support GATK-compatible VCF output format.

There are 2 errors which can happen when running GATK Variant Annotator
with a SnpEff result file as input:
- in GATK2: "The version of SnpEff used to generate the SnpEff input
file (3.x) is not currently supported by the GATK, and was not run in
GATK compatibility mode. Supported versions are: [2.0.5], as well as
later versions when run with the option -o gatk": this is fixed just by
selecting the "GATK-compatible VCF" output type;
- in GATK1: "The version of SnpEff used to generate the SnpEff input
file (x.x) is not currently supported by the GATK. Supported versions
are: [2.0.5]": this is fixed by selecting the GATK-compatible VCF output
type and also the "Compatible with GATK 1.x" checkbox.
Add log output. Better help.
Add wrapper for SnpSift varType.
Add wrapper for SnpSift dbNSFP.
Require SnpEff 3.6 .
.extra_files_path changed to .files_path
Add the 3 CADD scores (free only for non-commercial use!)
typos with file_path replacement have been fixed
migrate to new the citation tag
add msigdb loc file entry to tool_data_table
add msigdb database loc file
Fix and use snpeff_msigdb_database data table.
Warn about license dbNSFP license. Remove Orione paper citation.