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try:
from typing import Final
HAVE_FINAL = True
except ImportError:
HAVE_FINAL = False
from pysam.utils import PysamDispatcher
_BCFTOOLS_DISPATCH = [
"index",
"annotate",
"concat",
"convert",
"isec",
"merge",
"norm",
"plugin",
"query",
"reheader",
"sort",
"view",
"head",
"call",
"consensus",
"cnv",
"csq",
"filter",
"gtcheck",
"mpileup",
"roh",
"stats"]
def _wrap_command(dispatch: str) -> PysamDispatcher:
return PysamDispatcher("bcftools", dispatch, ())
if not HAVE_FINAL:
# instantiate bcftools commands as python functions
for cmd in _BCFTOOLS_DISPATCH:
globals()[cmd] = PysamDispatcher("bcftools", cmd, None)
else:
# python >=3.8
index: Final[PysamDispatcher] = _wrap_command("index")
annotate: Final[PysamDispatcher] = _wrap_command("annotate")
concat: Final[PysamDispatcher] = _wrap_command("concat")
convert: Final[PysamDispatcher] = _wrap_command("convert")
isec: Final[PysamDispatcher] = _wrap_command("isec")
merge: Final[PysamDispatcher] = _wrap_command("merge")
norm: Final[PysamDispatcher] = _wrap_command("norm")
plugin: Final[PysamDispatcher] = _wrap_command("plugin")
query: Final[PysamDispatcher] = _wrap_command("query")
reheader: Final[PysamDispatcher] = _wrap_command("reheader")
sort: Final[PysamDispatcher] = _wrap_command("sort")
view: Final[PysamDispatcher] = _wrap_command("view")
head: Final[PysamDispatcher] = _wrap_command("head")
call: Final[PysamDispatcher] = _wrap_command("call")
consensus: Final[PysamDispatcher] = _wrap_command("consensus")
cnv: Final[PysamDispatcher] = _wrap_command("cnv")
csq: Final[PysamDispatcher] = _wrap_command("csq")
filter: Final[PysamDispatcher] = _wrap_command("filter")
gtcheck: Final[PysamDispatcher] = _wrap_command("gtcheck")
mpileup: Final[PysamDispatcher] = _wrap_command("mpileup")
roh: Final[PysamDispatcher] = _wrap_command("roh")
stats: Final[PysamDispatcher] = _wrap_command("stats")
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