only use the reference_fasta config value if it is given, otherwise use the config file's value.
only use the reference_fasta config value if it is given, otherwise use the config file's value.

EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller,EichlerLab/pacbio_variant_caller