# 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",
           )