Parameter changes, Pedigree support, sanity check of files

- Renamed and syntaxed parameters
- Added environment variable 'env_up' for running with standard settings on uppmax
- Added support to read pedigree files
- Added automatic defaults when using the 'env_up' flag. Standard analysis can now be inititated using only "mip_align.pl -p b2010080 -familyid 33 -env_up 1".
- Added support for different capture files between samples when using pedigree to supply info.
- Added sanity check for files needed by each program. Run will terminate if file(s) is lacking.
- Added complete cmd line recreation to master_logg, enabling instance modifications before rerun.