added check to rna-seq step
Merge branch 'master' of ssh://git/srv/git/genome
forgot to push
add profile item status to ShowConfig
updated jenkins submodule to 3c0805d
cut down on error messages from bam-readcount
Commit after resolve_bed_for_reference since it can create SRs
clin-seq - bless new test build
update test dir
minor update to cnv calling
fix fn
add Clinseq class to gmt analysis
add GMB ClinSeq
update cnv calling parameters
revert changes to prior value.
update exome cnv calling
update test-dir and fix small bug
update clinseq blessed-cnmops updated
Squashed 'lib/perl/Genome/Model/Tools/Germline/gstat/' changes from 5482dd7..4d208d9

4d208d9 whitespace
bbf7ed4 solving mixed types of covar problem for binary trait in call.skat()

git-subtree-dir: lib/perl/Genome/Model/Tools/Germline/gstat
git-subtree-split: 4d208d908305f22bb1c0249e7074a9f87a30694a
Subtree merge of gstat repo from Qunyuan
remove spaces from dir names