Changed headers, added local exome, bumped clinical Db:s

- Added program checks for active programs
- Added the -numBad value (>=.GATK.2.7)
- Added local exome Db in intersectCollect
- Added sampleID to IntersectCollect -s
- Changed flag -s (select) to -sl (ranking)
- Removed IDN_GT_Call header. Now prints IDN:SampleID in header instead.
- Removed :PASS|:Pres from GT Call and added into separate column.
- Removed \:S+ in GT call check rank_filter.pl to accommodate GT format change
- Changed to dbIEM.v1.2.txt
- Added Disease_Gene_Model to output from dbIEM.
- Changed to dbEP.v.1.txt
- Added Disease_Gene_Model to output from dbEP.
- Changed multiple entries in intersectcollect master template and select master template to accommodate automatic entries into dbCV facilitating decoupling of position in dbCV.
- Decapreated "nocmdinput" in DefineParameters - now set in sub instead.
Minor changes
correcting bugs (Henrik)
merge conflicts