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.. automodule:: ngsfilter
:py:mod:`ngsfilter` specific options
------------------------------------
.. cmdoption:: -t, --tag-list
Used to specify the file containing the samples description (with tags, primers, sample names,...)
.. cmdoption:: -u, --unidentified
Filename used to store the sequences unassigned to any sample
.. cmdoption:: -e, --error
Used to specify the number of errors allowed for matching primers [default = 2]
.. include:: ../optionsSet/inputformat.txt
.. include:: ../optionsSet/outputformat.txt
.. include:: ../optionsSet/defaultoptions.txt
:py:mod:`ngsfilter` added sequence attributes
---------------------------------------------
.. hlist::
:columns: 3
- :doc:`avg_quality <../attributes/avg_quality>`
- :doc:`complemented <../attributes/complemented>`
- :doc:`cut <../attributes/cut>`
- :doc:`direction <../attributes/direction>`
- :doc:`error <../attributes/error>`
- :doc:`experiment <../attributes/experiment>`
- :doc:`forward_match <../attributes/forward_match>`
- :doc:`forward_primer <../attributes/forward_primer>`
- :doc:`forward_score <../attributes/forward_score>`
- :doc:`forward_tag <../attributes/forward_tag>`
- :doc:`head_quality <../attributes/head_quality>`
- :doc:`mid_quality <../attributes/mid_quality>`
- :doc:`partial <../attributes/partial>`
- :doc:`reverse_match <../attributes/reverse_match>`
- :doc:`reverse_primer <../attributes/reverse_primer>`
- :doc:`reverse_score <../attributes/reverse_score>`
- :doc:`reverse_tag <../attributes/reverse_tag>`
- :doc:`sample <../attributes/sample>`
- :doc:`seq_length <../attributes/seq_length>`
- :doc:`seq_length_ori <../attributes/seq_length_ori>`
- :doc:`status <../attributes/status>`
- :doc:`tail_quality <../attributes/tail_quality>`
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