Package Bio :: Package Sequencing :: Package Applications :: Module _samtools :: Class SamtoolsCalmdCommandline
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Class SamtoolsCalmdCommandline

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                     object --+    
Application.AbstractCommandline --+

Command line wrapper for samtools calmd.

Generate the MD tag, equivalent to:

$ samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>

See for more details


>>> from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
>>> input_bam = "/path/to/aln.bam"
>>> reference_fasta = "/path/to/reference.fasta"
>>> calmd_cmd = SamtoolsCalmdCommandline(input_bam=input_bam,
...                                      reference=reference_fasta)
>>> print(calmd_cmd)
samtools calmd /path/to/aln.bam /path/to/reference.fasta
Instance Methods [hide private]
__init__(self, cmd='samtools', **kwargs)
Initialize the class.
source code

Inherited from Application.AbstractCommandline: __call__, __repr__, __setattr__, __str__, set_parameter

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __sizeof__, __subclasshook__

Class Variables [hide private]

Inherited from Application.AbstractCommandline: parameters

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, cmd='samtools', **kwargs)

source code 
Initialize the class.
Overrides: object.__init__