initialize reference inside function so it can be accessible when run…

…ning pca via a python script

gwaspy/pca/pca.py

@@ -18,6 +18,8 @@ def pca(
     if not out_dir:
         raise Exception('\nOutput directory where files will be saved is not specified')
 
+    hl.default_reference(new_default_reference=reference)
+
     if pca_type == 'project':
         print('\nRunning PCA using projection method')
 
@@ -85,8 +87,6 @@ def main():
     if not args.prob:
         print(f'No prob value specified, {args.prob} will be used')
 
-    hl.default_reference(new_default_reference=args.reference)
-
     pca(ref_dirname=args.ref_dirname, ref_basename=args.ref_basename, ref_info=args.ref_info, reference=args.reference,
         pca_type=args.pca_type, input_type=args.input_type, data_dirname=args.data_dirname,
         data_basename=args.data_basename, maf=args.maf, hwe=args.hwe, call_rate=args.geno, ld_cor=args.ld_cor,