Adding new variant calling script
Regexp to get resources
Adding exception for no file found.
Adding .gz file endings
Missed .* at beging of regexp
Added debugging log messages
The files need to be unzipped, so remove .gz
After discussions with Pallo, adding .gz again.

And fixing exception when no file is matched by the regexp to include the regexp.
Refactoring for readability
And removing .gz because it didn't work...
Added "hidded" import
Merge branch 'devel' into newVariantCallingScript
(Almost) working prototype

There is still a lot of checking of the parameters left to do, but the script basically seems to be working, with one exception. It breaks down when attempting to apply the variant recalibration to indels. I have as of yet not been able to figure out why that is.
Changed log level from info to debug.
Adding eclipse project stuff to repo

It really bugs me to have to manually setup this stuff everytime
Merge branch 'devel' into newVariantCallingScript
Add FixMatePairInfo to script
Added indexing as part of workflow
Changed location of MD5 db
Clean up of unused code