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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Main entry point for sequencing related command line application wrappers."""
from ._Novoalign import NovoalignCommandline
from ._bwa import BwaIndexCommandline, BwaAlignCommandline, BwaSamseCommandline
from ._bwa import BwaSampeCommandline, BwaBwaswCommandline, BwaMemCommandline
from ._samtools import SamtoolsViewCommandline, SamtoolsCalmdCommandline
from ._samtools import SamtoolsCatCommandline, SamtoolsFaidxCommandline
from ._samtools import SamtoolsFixmateCommandline, SamtoolsIdxstatsCommandline
from ._samtools import SamtoolsIndexCommandline, SamtoolsMergeCommandline
from ._samtools import SamtoolsMpileupCommandline, SamtoolsPhaseCommandline
from ._samtools import SamtoolsReheaderCommandline, SamtoolsRmdupCommandline
from ._samtools import SamtoolsVersion0xSortCommandline, SamtoolsVersion1xSortCommandline, SamtoolsTargetcutCommandline
from ._samtools import SamtoolsVersion0xSortCommandline as SamtoolsSortCommandline
# Make this explicit, then they show up in the API docs
__all__ = ("BwaIndexCommandline",
"BwaAlignCommandline",
"BwaSamseCommandline",
"BwaSampeCommandline",
"BwaBwaswCommandline",
"BwaMemCommandline",
"SamtoolsViewCommandline",
"SamtoolsCalmdCommandline",
"SamtoolsCatCommandline",
"SamtoolsFaidxCommandline",
"SamtoolsFixmateCommandline",
"SamtoolsIdxstatsCommandline",
"SamtoolsIndexCommandline",
"SamtoolsMergeCommandline",
"SamtoolsMpileupCommandline",
"SamtoolsPhaseCommandline",
"SamtoolsReheaderCommandline",
"SamtoolsRmdupCommandline",
"SamtoolsSortCommandline",
"SamtoolsVersion0xSortCommandline",
"SamtoolsVersion1xSortCommandline",
"SamtoolsTargetcutCommandline",
)
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