29db4abdbeb839340ac5b0caf934ebda93892934,cnvlib/commands.py,,,#,1294

Before Change

                [Default: use the sample ID, taken from the file name])
P_export_bed.add_argument("--ploidy", type=int, default=2,
        help="Ploidy of the sample cells. [Default: %(default)d]")
P_export_bed.add_argument("-x", "--sample-sex", "-g", "--gender",
        dest="sample_sex",
        choices=("m", "y", "male", "Male", "f", "x", "female", "Female"),
        help=Specify the sample"s chromosomal sex as male or female.
                (Otherwise guessed from X and Y coverage).)
P_export_bed.add_argument("--show",
        choices=("ploidy", "variant", "all"), default="ploidy",
        help=Which segmented regions to show:
                "all" = all segment regions;

After Change

// export ----------------------------------------------------------------------

P_export = AP_subparsers.add_parser("export",
        help=Convert CNVkit output files to another format.)
P_export_subparsers = P_export.add_subparsers(
        help="Export formats (use with -h for more info).")


// BED special case: multiple samples"s segments, like SEG
def _cmd_export_bed(args):

Instances