Factor out base-class for Varscan pileup commands
Add Varscan Indel command and tests
Add build accessor for target_region_set_name input
updated ur submodule to 406a3a2
updated workflow submodule to 3a6f56c
Changing method call approach throughout clin-seq for module Util.pm that has not yet been incorporated into a proper class
ClinSeq: Found another file that relied on Util.pm
Changing method call approach throughout clin-seq for module RnaSeqUtil.pm that has not yet been incorporated into a proper class
updated converge scripts inside Clinseq, reorganized original scripts
remove old original-scripts and update directory name
remove defaults that are now specified in /etc/profile.d/genome.sh
GENOME_DEV_MODE and UR_DBI_NO_COMMIT are not so synonymous
Remove duplicate copies of move perl modules
Remove incorrect documentation
Bugfix Vcf::Differ does not crash when file sizes differ
remove unused code from clinseq utility
fix broken use lib statements
further fixes to clin-seq tests to account for reorganization of modules