File ending and chain fixes

- Added chain parameter to defineParameters
- Connected chains for submission and file endings.
- Added generalized and continuous file ending support for chain forks (inherits from MAIN at point of separation)
- Added missing FILTER= to last IDN. (thx @Mats)
- Moved Phasing modules to correct place in script
Automated Rapid mode, Program prerequisites, PLINK-format for pedigree files, fixed consisten chr prefix usage, fixed GATKVareEvalExome

- Fully automated rapid mode enabled
- SBATCH header is now handled by new subroutine program prerequisites
- Fixed exome selection in GATK Vareval
- Positioned execution order of GATK VarevalExome to after vcf merge
- Fixed consistent use of chromosome prefix throughout mip
- Pedigree files should now be supplied in PLINK format
- Minor bug fixes
Merge branch 'release/v1.3'