29db4abdbeb839340ac5b0caf934ebda93892934,cnvlib/commands.py,,,#,999

Before Change

// metrics ---------------------------------------------------------------------

do_metrics = public(metrics.do_metrics)


def _cmd_metrics(args):
    Compute coverage deviations and other metrics for self-evaluation.

After Change

P_gainloss.add_argument("-t", "--threshold", type=float, default=0.2,
        help=Copy number change threshold to report a gene gain/loss.
                [Default: %(default)s])
P_gainloss.add_argument("-m", "--min-probes", type=int, default=3,
        help=Minimum number of covered probes to report a gain/loss.
                [Default: %(default)d])
P_gainloss.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_gainloss.add_argument("-y", "--male-reference", action="store_true",

Instances