Package Bio :: Package Sequencing :: Package Applications
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Source Code for Package Bio.Sequencing.Applications

 1  # This code is part of the Biopython distribution and governed by its 
 2  # license.  Please see the LICENSE file that should have been included 
 3  # as part of this package. 
 4  # 
 5   
 6  """Main entry point for application command line wrappers related to sequencing. 
 7  """ 
 8  from ._Novoalign import NovoalignCommandline 
 9  from ._bwa import BwaIndexCommandline, BwaAlignCommandline, BwaSamseCommandline 
10  from ._bwa import BwaSampeCommandline, BwaBwaswCommandline 
11  from ._samtools import SamtoolsViewCommandline, SamtoolsCalmdCommandline 
12  from ._samtools import SamtoolsCatCommandline, SamtoolsFaidxCommandline 
13  from ._samtools import SamtoolsFixmateCommandline, SamtoolsIdxstatsCommandline 
14  from ._samtools import SamtoolsIndexCommandline, SamtoolsMergeCommandline 
15  from ._samtools import SamtoolsMpileupCommandline, SamtoolsPhaseCommandline 
16  from ._samtools import SamtoolsReheaderCommandline, SamtoolsRmdupCommandline 
17  from ._samtools import SamtoolsVersion0xSortCommandline, SamtoolsVersion1xSortCommandline, SamtoolsTargetcutCommandline 
18  from ._samtools import SamtoolsVersion0xSortCommandline as SamtoolsSortCommandline 
19   
20   
21  # Make this explicit, then they show up in the API docs 
22  __all__ = ("BwaIndexCommandline", 
23             "BwaAlignCommandline", 
24             "BwaSamseCommandline", 
25             "BwaSampeCommandline", 
26             "BwaBwaswCommandline", 
27             "SamtoolsViewCommandline", 
28             "SamtoolsCalmdCommandline", 
29             "SamtoolsCatCommandline", 
30             "SamtoolsFaidxCommandline", 
31             "SamtoolsFixmateCommandline", 
32             "SamtoolsIdxstatsCommandline", 
33             "SamtoolsIndexCommandline", 
34             "SamtoolsMergeCommandline", 
35             "SamtoolsMpileupCommandline", 
36             "SamtoolsPhaseCommandline", 
37             "SamtoolsReheaderCommandline", 
38             "SamtoolsRmdupCommandline", 
39             "SamtoolsSortCommandline", 
40             "SamtoolsVersion0xSortCommandline", 
41             "SamtoolsVersion1xSortCommandline", 
42             "SamtoolsTargetcutCommandline", 
43             ) 
44