Commit f845f3cd authored by Hanna  JULIENNE's avatar Hanna JULIENNE

add parameter to parser

parent 47cb3a06
Pipeline #11208 passed with stages
in 1 minute and 11 seconds
......@@ -14,7 +14,7 @@ def launch_chromosome_imputation(args):
args (dict): Argument parsed from the command line see the
__main__.add_chromosome_imputation_argument(parser) function.
"""
save_chromosome_imputation(args.gwas, args.chrom, args.window_size, args.buffer_size, args.l2_regularization, args.eigen_threshold, args.zscore_folder, args.ref_folder, args.ld_folder, args.output_folder, args.R2_threshold)
save_chromosome_imputation(args.gwas, args.chrom, args.window_size, args.buffer_size, args.l2_regularization, args.eigen_threshold, args.zscore_folder, args.ref_folder, args.ld_folder, args.output_folder, args.R2_threshold, ref_panel_suffix=args.ref_panel_suffix)
def add_chromosome_imputation_argument():
......@@ -33,6 +33,7 @@ def add_chromosome_imputation_argument():
parser.add_argument('--eigen-threshold', help= "threshold under which eigen vectors are removed for the computation of the pseudo inverse", default = 0.1)
parser.add_argument('--R2-threshold', help= "R square (imputation quality) threshold bellow which SNPs are filtered from the output", default = 0.6)
parser.add_argument('--ref-panel-suffix', help= "end of the suffix for the reference panel files", default = ".eur.1pct.bim")
parser.set_defaults(func=launch_chromosome_imputation)
return(parser)
......
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