)
parser.add_argument(
"--coverage-threshold",
type=int,
required=False,
default=5,
help=(
"A junction passes the filter if it is covered by at least "
"this many reads in a single sample; if the junction meets "
"neither this criterion nor the --sample-fraction criterion, "
"it is filtered out; use -1 to disable"
),
)
# Add command-line arguments for dependencies
manifest.add_args(parser)
"""Now collect arguments. While the variable args declared below is
global, properties of args are also arguments of the go() function so
different command-line arguments can be passed to it for unit tests."""
args = parser.parse_args(sys.argv[1:])
if __name__ == "__main__" and not args.test:
start_time = time.time()
manifest_object = manifest.LabelsAndIndices(os.path.expandvars(args.manifest))
input_line_count, output_line_count = go(
manifest_object=manifest_object,
input_stream=sys.stdin,
output_stream=sys.stdout,
sample_fraction=args.sample_fraction,
coverage_threshold=args.coverage_threshold,
const=True,
default=False,
help='Print exon intervals')
parser.add_argument('--drop-deletions',
action='store_const',
const=True,
default=False,
help='Drop deletions from coverage vectors')
parser.add_argument('--output-bam-by-chr',
action='store_const',
const=True,
default=False,
help='Final BAMs will be output by chromosome')
bowtie.add_args(parser)
manifest.add_args(parser)
partition.add_args(parser)
from alignment_handlers import add_args as alignment_handlers_add_args
alignment_handlers_add_args(parser)
# Collect Bowtie arguments, supplied in command line after the -- token
argv = sys.argv
bowtie_args = ''
in_args = False
for i, argument in enumerate(sys.argv[1:]):
if in_args:
bowtie_args += argument + ' '
if argument == '--':
argv = sys.argv[:i + 1]
in_args = True
'''Now collect other arguments. While the variable args declared below is