def parse_args(args):
"""
Takes in the command-line arguments list (args), and returns a nice argparse
result with fields for all the options.
Borrows heavily from the argparse documentation examples:
<http://docs.python.org/library/argparse.html>
"""
# Construct the parser (which is stored in parser)
# Module docstring lives in __doc__
# See http://python-forum.com/pythonforum/viewtopic.php?f=3&t=36847
# And a formatter class so our examples in the docstring look good. Isn't it
# convenient how we already wrapped it to 80 characters?
# See http://docs.python.org/library/argparse.html#formatter-class
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
# Add all the toil-vg options
toilvgfacade.add_options(parser)
# Add the Toil options so the job store is the first argument
Job.Runner.addToilOptions(parser)
parser.add_argument("--contig", default=None,
help="download just pairs touching this contig or its alts/randoms")
parser.add_argument("--sam_url", default=[], action="append",
help="URL to download reads from, accessible from Toil nodes")
# Output
parser.add_argument("out_url",
help="file: or other Toil-supported URL to place results in")
# The command line arguments start with the program name, which we don't
# want to treat as an argument for argparse. So we remove it.
args = args[1:]
return parser.parse_args(args)
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