nargs="+",
help="SV types to report",
default=SVS_SUPPORTED,
choices=SVS_SUPPORTED)
out_parser.add_argument(
"--enable_per_tool_output",
action="store_true",
help="Enable output of merged SVs for individual tools")
work_parser = parser.add_argument_group("Running environment options")
work_parser.add_argument("--workdir",
help="Scratch directory for working",
default="work",
required=False)
work_parser.add_argument("--num_threads",
help="Number of threads to use",
type=int,
default=1)
work_parser.add_argument("--outdir",
help="Output directory",
required=True)
other_parser = parser.add_argument_group("Other options")
other_parser.add_argument('--version',
action='version',
version='%(prog)s ' + __version__)
args = parser.parse_args()
sys.exit(run_metasv(args))
out_parser = parser.add_argument_group("Output options")
out_parser.add_argument("--enable_per_tool_output", action="store_true",
help="Enable output of merged SVs for individual tools")
work_parser = parser.add_argument_group("Running environment options")
work_parser.add_argument("--workdir", help="Scratch directory for working", default="work", required=False)
work_parser.add_argument("--num_threads", help="Number of threads to use", type=int, default=1)
work_parser.add_argument("--outdir", help="Output directory", required=True)
other_parser = parser.add_argument_group("Other options")
other_parser.add_argument('--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args()
sys.exit(run_metasv(args.sample, args.reference, pindel_vcf=args.pindel_vcf, pindel_native=args.pindel_native,
breakdancer_vcf=args.breakdancer_vcf, breakdancer_native=args.breakdancer_native,
breakseq_vcf=args.breakseq_vcf, breakseq_native=args.breakseq_native,
cnvnator_vcf=args.cnvnator_vcf,
cnvnator_native=args.cnvnator_native, gatk_vcf=args.gatk_vcf,
gaps=args.gaps, filter_gaps=args.filter_gaps, keep_standard_contigs=args.keep_standard_contigs,
wiggle=args.wiggle, overlap_ratio=args.overlap_ratio,
workdir=args.workdir, outdir=args.outdir, boost_ins=args.boost_ins, bam=args.bam,
chromosomes=args.chromosomes, num_threads=args.num_threads, spades=args.spades, age=args.age,
disable_assembly=args.disable_assembly, minsvlen=args.minsvlen, inswiggle=args.inswiggle,
enable_per_tool_output=args.enable_per_tool_output, min_support=args.min_ins_support,
min_support_frac=args.min_ins_support_frac, max_intervals=args.max_ins_intervals,
disable_deletion_assembly=args.disable_deletion_assembly,
stop_spades_on_fail=args.stop_spades_on_fail, gt_window=args.gt_window, gt_normal_frac=args.gt_normal_frac, isize_mean=args.isize_mean, isize_sd=args.isize_sd, extraction_max_read_pairs=args.extraction_max_read_pairs))
as_parser.add_argument("--min_del_subalign_len", help="Minimum length of deletion sub-alginment", type=int,
default=MIN_DEL_SUBALIGN_LENGTH)
as_parser.add_argument("--age_window", help="Window size for AGE to merge nearby breakpoints", type=int,
default=AGE_WINDOW_SIZE)
as_parser.add_argument("--boost_sc", help="Use soft-clips for improving breakpoint detection",
action="store_true")
gt_parser = parser.add_argument_group("Genotyping options")
gt_parser.add_argument("--gt_window", type=int, default=GT_WINDOW, help="Window for genotyping")
gt_parser.add_argument("--gt_normal_frac", type=float, default=GT_NORMAL_FRAC,
help="Min. fraction of reads supporting reference for genotyping")
out_parser = parser.add_argument_group("Output options")
out_parser.add_argument("--svs_to_report", nargs="+", help="SV types to report", default=SVS_SUPPORTED,
choices=SVS_SUPPORTED)
out_parser.add_argument("--enable_per_tool_output", action="store_true",
help="Enable output of merged SVs for individual tools")
work_parser = parser.add_argument_group("Running environment options")
work_parser.add_argument("--workdir", help="Scratch directory for working", default="work")
work_parser.add_argument("--num_threads", help="Number of threads to use", type=int, default=1)
work_parser.add_argument("--outdir", help="Output directory", required=True)
other_parser = parser.add_argument_group("Other options")
other_parser.add_argument('--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args()
args.svs_to_assemble = set(args.svs_to_assemble) & set(args.svs_to_report)
args.svs_to_softclip = set(args.svs_to_softclip) & set(args.svs_to_report)
sys.exit(run_metasv(args))
help="Chromosome list to process. If unspecified, then all chromosomes will be considered.",
nargs="+", default=[])
parser.add_argument("--num_threads", help="Number of threads to use", type=int, default=1)
parser.add_argument("--outdir", help="Output directory", required=True)
parser.add_argument("--spades", help="Path to SPAdes executable", required=False)
parser.add_argument("--age", help="Path to AGE executable", required=False)
parser.add_argument("--disable_assembly", action="store_true", help="Disable assembly")
parser.add_argument("--enable_per_tool_output", action="store_true",
help="Enable output of merged SVs for individual tools")
parser.add_argument("--disable_deletion_assembly", action="store_true", help="Disable assembly for deletions")
parser.add_argument("--stop_spades_on_fail", action="store_true", help="Abort on SPAdes failure")
parser.add_argument('--version', action='version', version='%(prog)s ' + __version__)
args = parser.parse_args()
sys.exit(run_metasv(args.sample, args.reference, pindel_vcf=args.pindel_vcf, pindel_native=args.pindel_native,
breakdancer_vcf=args.breakdancer_vcf, breakdancer_native=args.breakdancer_native,
breakseq_vcf=args.breakseq_vcf, breakseq_native=args.breakseq_native,
cnvnator_vcf=args.cnvnator_vcf,
cnvnator_native=args.cnvnator_native, gatk_vcf=args.gatk_vcf,
gaps=args.gaps, filter_gaps=args.filter_gaps, keep_standard_contigs=args.keep_standard_contigs,
wiggle=args.wiggle, overlap_ratio=args.overlap_ratio,
workdir=args.workdir, outdir=args.outdir, boost_ins=args.boost_ins, bam=args.bam,
chromosomes=args.chromosomes, num_threads=args.num_threads, spades=args.spades, age=args.age,
disable_assembly=args.disable_assembly, minsvlen=args.minsvlen, inswiggle=args.inswiggle,
enable_per_tool_output=args.enable_per_tool_output, min_support=args.min_ins_support,
min_support_frac=args.min_ins_support_frac, max_intervals=args.max_ins_intervals,
disable_deletion_assembly=args.disable_deletion_assembly,
stop_spades_on_fail=args.stop_spades_on_fail))