Added a exon flagstat

Adding more output files to bamstats

compiling ssp-template files with scalate

no need to copy the template from classpath to a file, TemplateEngine is able to access the files also from there, and it's able also to find precompiled template classes when it's given the path to the ssp template

Test fail on format/git issues

# Conflicts:
#	Jenkinsfile

Changed VCFstats to check whether outputDir is a valid directory.

Remove hard-coded settings in XhmmMatrix.

Improvement biopet 561

Fix biopet 585

Fixed that the timeout in on node time instead of including queue time