EX-96 (cgates): Adjusted test to prevent spurious errors
EX-128 (cgates): Removed extraneous code, orphaned test files.
EX-129 (cgates): Adjust VarScan high-confidence to use fpfilter.pass
EX-129 (cgates): Adjusted to use fpfilter.pass
EX-129 (cgates): Minor logging adjustments
EX-96 (cgates): Adjust gene_rollup. Adjust jacqaurd temp dir handling.
EX-96 (cgates): Disabling temp dir handling until we can make it work
EX-96 (cgates): Disabling temp dir handling until we can make it work
Merge remote-tracking branch 'origin/develop' into
ex-126_add_functional_tests

Conflicts:
	jacquard/jacquard.py
	test/filter_hc_somatic_test.py