Clean up
Update mip.pl
Merge remote-tracking branch 'upstream/master'
Added coverage module, started chanjo addition
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
Chanjo module is separate, removed nocmdinput, not running by def
more inputs to sub chanjo, FID
Require chanjo sub since using MIP subs
Added template for the no prev merge case to chanjo sub
Close file handle, corrected spelling... :(
Merge pull request #5 from robinandeer/develop

Added chanjo
Small changes
+ Added sub template
* Writing all samples to one SBATCH script
+ Added import to family-specific sqlite db
TODO: change storePath to ccdsPath
Merge pull request #6 from robinandeer/develop

Added subroutine template
Added sub InfilesReformat2 add to sampleInfo, added sub SampleInfoQC, added program qcCollect.pl to repo
Merge branch 'develop' of https://github.com/henrikstranneheim/MIP

Conflicts:
	mip.pl~
changes to mip.pl