Allow to relax pre-processing filter criteria

[marcelm]

Originally reported by: Marcel Martin (Bitbucket: marcelm, GitHub: marcelm)

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In particular, requiring that the V coverage is at last 90% is not appropriate when the 5' primers are within the V segment.

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• Bitbucket: https://bitbucket.org/igdiscover/igdiscover/issue/25

[marcelm]

Original comment by Marcel Martin (Bitbucket: marcelm, GitHub: marcelm):

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Make the pre-processing filter configurable

Closes #25

[marcelm]

Original comment by Marcel Martin (Bitbucket: marcelm, GitHub: marcelm):

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I’ve now made this configurable. Here is the new section in the igdiscover.yaml:

# Preprocessing filter settings. This filter is always applied directly after running IgBLAST,
# even if no gene discovery is requested.
#
preprocessing_filter:
  v_coverage: 90   # Match must cover V gene by at least this percentage
  j_coverage: 60   # Match must cover J gene by at least this percentage
  v_evalue: 0.001  # Highest allowed V gene match E-value

Allowing the user to define a V-gene region is a bit harder to implement, so I have chosen this way.

[marcelm]

Original comment by Ufuk Kirik (Bitbucket: ukirik, GitHub: ukirik):

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An alternative to decreasing the 90% coverage criteria would be to allow the user to define a region in the V-gene which are used when comparing sequences to the target database.