Exit and give a descriptive error when config file does not have all required arguments

[ozlemmuslu]

The following should be found in config file:

REF_DIR
MODELS_DIR
KNOWN_INDELS1
KNOWN_INDELS2
DBSNP
REF
EXOME_BED

KNOWN_INDELS2 and EXOME_BED can be left empty.
KNOWN_INDELS1 and DBSNP can be empty if BAM preprocessing is skipped
REF should be given in all cases
We need to check behaviour when REF_DIR/MODELS_DIR are left empty (probably writes in current directory)