Copy over variant_type, raw_output_file, raw_inputs, raw_input_for_chromosome, generate_standard_files

code-deduplication: gsanders
Copied over variant_type, raw_output_file, raw_inputs, raw_input_for_chromosome

code-deduplication: gsanders
Move up default_chromosomes

code-deduplication: gsanders
Move up raw_output_file

code-deduplication: gsanders
Move up raw_inputs

code-deduplication: gsanders
Move up raw_input_for_chromosome

code-deduplication: gsanders
Move up _generate_standard_files

code-deduplication: gsanders
Move up _ensure_chromosome_list_set

code-deduplication: gsanders
Move up chromosome_list

code-deduplication: gsanders