29db4abdbeb839340ac5b0caf934ebda93892934,cnvlib/commands.py,,,#,389

Before Change

P_reference.add_argument("references", nargs="*",
        help=Normal-sample target or antitarget .cnn files, or the
                directory that contains them.)
P_reference.add_argument("-f", "--fasta",
        help="Reference genome, FASTA format (e.g. UCSC hg19.fa)")
P_reference.add_argument("-o", "--output", help="Output file name.")
P_reference.add_argument("-y", "--male-reference", action="store_true",
        help=Create a male reference: shift female samples" chrX
                log-coverage by -1, so the reference chrX average is -1.
                Otherwise, shift male samples" chrX by +1, so the reference chrX
                average is 0.)
P_reference.add_argument("-x", "--sample-sex", "-g", "--gender",
        dest="sample_sex",
        choices=("m", "y", "male", "Male", "f", "x", "female", "Female"),
        help=Specify the chromosomal sex of all given samples as male or
                female. (Default: guess each sample from coverage of X and Y
                chromosomes).)

P_reference_flat = P_reference.add_argument_group(
    "To construct a generic, \"flat\" copy number reference with neutral "
    "expected coverage")
P_reference_flat.add_argument("-t", "--targets",
        help="Target intervals (.bed or .list)")
P_reference_flat.add_argument("-a", "--antitargets",
        help="Antitarget intervals (.bed or .list)")

P_reference_bias = P_reference.add_argument_group(
    "To disable specific automatic bias corrections")
P_reference_bias.add_argument("--no-gc", dest="do_gc", action="store_false",
        help="Skip GC correction.")
P_reference_bias.add_argument("--no-edge", dest="do_edge", action="store_false",
        help="Skip edge-effect correction.")
P_reference_bias.add_argument("--no-rmask", dest="do_rmask", action="store_false",
        help="Skip RepeatMasker correction.")
P_reference.set_defaults(func=_cmd_reference)


// fix -------------------------------------------------------------------------

After Change

P_coverage = AP_subparsers.add_parser("coverage", help=_cmd_coverage.__doc__)
P_coverage.add_argument("bam_file", help="Mapped sequence reads (.bam)")
P_coverage.add_argument("interval", help="Intervals (.bed or .list)")
P_coverage.add_argument("-c", "--count", action="store_true",
        help=Get read depths by counting read midpoints within each bin.
                (An alternative algorithm).)
P_coverage.add_argument("-q", "--min-mapq", type=int, default=0,
        help=Minimum mapping quality score (phred scale 0-60) to count a read
                for coverage depth.  [Default: %(default)s])
P_coverage.add_argument("-o", "--output", help=Output file name.)
P_coverage.add_argument("-p", "--processes",
        nargs="?", type=int, const=0, default=1,
        help=Number of subprocesses to calculate coverage in parallel.
                Without an argument, use the maximum number of available CPUs.
                [Default: use 1 process])
P_coverage.set_defaults(func=_cmd_coverage)


// reference -------------------------------------------------------------------

Instances