fix commit

impute_jass/impute_jass/__main__.py

@@ -14,14 +14,14 @@ def launch_chromosome_imputation(args):
 
     z_file = "{0}/z_{1}_{2}.txt".format(args.zscore_folder, args.gwas, args.chrom)
     zscore = pd.read_csv(z_file)
-    imputer.chromosome_imputation(args.chrom, zscore, ref_panel, ld_folder)
+    imputer.chromosome_imputation(args.chrom, zscore, args.ref_panel, args.ld_folder)
 
 def add_chromosome_imputation_argument(parser):
     parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format")
     parser.add_argument('--gwas', required=True, help= "GWAS to impute to the consortia_trait format")
 
     parser.add_argument('--ref-folder', required=True, help= "reference panel location (used to determine which snp to impute)")
-    parser.add_argument('--LD-folder', required=True, help= "Location  LD correlation matrices")
+    parser.add_argument('--ld-folder', required=True, help= "Location  LD correlation matrices")
     parser.add_argument('--zscore-folder', required=True, help= "Location of the zscore files of the gwases to impute")
     parser.add_argument('--output-folder', required=True, help= "Location of the impute zscore files")