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