/usr/lib/python2.7/dist-packages/pbalign/ccs.py is in python-pbalign 0.3.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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VERY thin wrapper on top of pbalign to provide a tool contract-driven task
specific to CCS reads.
"""
import sys
from pbcommand.models import FileTypes
from pbalign import pbalignrunner
import pbalign.options
class Constants(pbalign.options.Constants):
TOOL_ID = "pbalign.tasks.pbalign_ccs"
DRIVER_EXE = "python -m pbalign.ccs --resolved-tool-contract"
INPUT_FILE_TYPE = FileTypes.DS_CCS
OUTPUT_FILE_TYPE = FileTypes.DS_ALIGN_CCS
# some modified defaults
ALGORITHM_OPTIONS_DEFAULT = "--minMatch 12 --bestn 10 --minPctSimilarity 70.0"
def get_parser():
return pbalign.options.get_contract_parser(Constants, ccs_mode=True)
def main(argv=sys.argv):
return pbalignrunner.main(
argv=argv,
get_parser_func=get_parser,
contract_runner_func=pbalignrunner.resolved_tool_contract_runner_ccs)
if __name__ == "__main__":
sys.exit(main())
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