INNER CODE UNIT · Python
main
MariaNattestad/assemblytics · assemblytics/cli.py:174
def main():
parser = argparse.ArgumentParser(
description="Assemblytics structural variant detection pipeline",
usage=USAGE,
)
parser.add_argument("-d", "--delta", help="MUMmer delta file (.delta or .delta.gz)", required=True)
parser.add_argument("-o", "--output_dir", help="Output directory for assemblytics_* result files (default: current directory)", default=".")
parser.add_argument("-l", "--unique_length", type=int, default=10000, help="Unique anchor length requirement (default: 10000)")
parser.add_argument("-min", "--minimum_size", type=int, default=50, help="Minimum variant size to call (default: 50)")
parser.add_argument("-max", "--maximum_size", type=int, default=10000, help="Maximum variant size to call (default: 10000)")
parser.add_argument(
"--long-range",
dest="long_range",
action="store_true",
help=(
"Also report long-range and inter-chromosomal candidate variants (events bigger "
"than --maximum_size, or spanning two different reference chromosomes) to a "
"separate assemblytics_long_range_variants.bed file. These are usually caused by "