f344df034cb674e198996da63d430287394242bd,cnvlib/commands.py,,,#,1442

Before Change

P_import_picard = AP_subparsers.add_parser("import-picard",
        help=_cmd_import_picard.__doc__)
P_import_picard.add_argument("targets", nargs="*", default=["."],
        help=Sample coverage .csv files (target and antitarget), or the
                directory that contains them.)
P_import_picard.add_argument("-d", "--output-dir", default=".",
        help="Output directory name.")
P_import_picard.set_defaults(func=_cmd_import_picard)

After Change

    return np.percentile(bins["log2"], [2.5, 97.5])


P_segmetrics = AP_subparsers.add_parser("segmetrics", help=_cmd_segmetrics.__doc__)
P_segmetrics.add_argument("cnarray",
        help=Bin-level copy ratio data file (*.cnn, *.cnr).)
P_segmetrics.add_argument("-s", "--segments", required=True,
        help="Segmentation data file (*.cns, output of the "segment" command).")
P_segmetrics.add_argument("--drop-low-coverage", action="store_true",
        help=Drop very-low-coverage bins before segmentation to avoid
                false-positive deletions in poor-quality tumor samples.)
P_segmetrics.add_argument("-o", "--output",
        help="Output table file name.")

P_segmetrics_stats = P_segmetrics.add_argument_group(
    "Statistics available")
P_segmetrics_stats.add_argument("--stdev", action="store_true",
        help="Standard deviation.")
P_segmetrics_stats.add_argument("--mad", action="store_true",
        help="Median absolute deviation (standardized).")
P_segmetrics_stats.add_argument("--iqr", action="store_true",
        help="Inter-quartile range.")
P_segmetrics_stats.add_argument("--bivar", action="store_true",
        help="Tukey"s biweight midvariance.")
P_segmetrics_stats.add_argument("--ci", action="store_true",
        help="Confidence interval (by bootstrap).")
P_segmetrics_stats.add_argument("--pi", action="store_true",
        help="Prediction interval.")

P_segmetrics.set_defaults(func=_cmd_segmetrics)

Instances