diff --git a/build_pop.py b/build_pop.py index 415e37c2ea76062a17b5ba8add60c0a7717659e0..8cfb3bc6d7b36489a34d0d9dd5ef7991ac71813c 100755 --- a/build_pop.py +++ b/build_pop.py @@ -28,8 +28,8 @@ def parse_args(): parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False) parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int) parser.add_argument("-o", "--output-directory", help="Output directory", default="res") - parser.add_argument("-e", "--erase-output", help="Delete output, if directory already exists", action='store_const', - const=True, default=False) + parser.add_argument("-e", "--force-outputdir", help="Delete output directory before start, if already exists", + action='store_const', const=True, default=False) parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True, default=False) parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", @@ -317,10 +317,10 @@ def confirm(deletions: dict, variants: dict): return input("Continue [Y/n]? ") in ["y", "Y", ""] -def init(output_dir, erase_output, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism, +def init(output_dir, force_outputdir, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism, coverage, read_len, insert_len_mean, insert_len_sd, threads, quiet=True): if os.path.isdir(output_dir): - if erase_output: + if force_outputdir: shutil.rmtree(output_dir) else: eprint("Error: output directory {0} already exists.".format(output_dir)) @@ -376,7 +376,7 @@ def main(): output_dir = args.output_directory haploid = args.haploid nb_inds = args.nb_inds - erase_output = args.erase_output + force_outputdir = args.force_outputdir proba_del = args.proba_del threads = args.threads force_polymorphism = args.force_polymorphism @@ -386,7 +386,7 @@ def main(): insert_len_sd = args.insert_len_sd quiet = args.quiet - init(output_dir, erase_output, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism, + init(output_dir, force_outputdir, sv_list, nb_inds, reference, proba_del, haploid, force_polymorphism, coverage, read_len, insert_len_mean, insert_len_sd, threads, quiet) if __name__ == '__main__':