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

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                     object --+    
Application.AbstractCommandline --+

Command line wrapper for samtools rmdup.

Remove potential PCR duplicates, equivalent to:

$ samtools rmdup [-sS] <> <out.bam>

See for more details


>>> from Bio.Sequencing.Applications import SamtoolsRmdupCommandline
>>> input_sorted_bam = "/path/to/"
>>> out_bam = "/path/to/out.bam"
>>> rmdup_cmd = SamtoolsRmdupCommandline(input_bam=input_sorted_bam,
...                                      out_bam=out_bam)
>>> print(rmdup_cmd)
samtools rmdup /path/to/ /path/to/out.bam
Instance Methods [hide private]
__init__(self, cmd='samtools', **kwargs)
Initialize the class.
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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__