ENH: extract-seq-segments add param "min_coverage"
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The Problem
extract-seq-segments
does not have a min_coverage
threshold exposed, so it is possible to extract sequences that may pass the %identity threshold but actually have very low coverage (I do not know off-hand what the default is, but we should set an explicit default either way).
Solution
Expose a min_coverage
parameter to specify the minimum amount of coverage of the reference that is required for a hit to pass.
This code should be relatively easy to expose — there is precedent with the vsearch-global
action in q2-feature-classifier that can be used as a template here. The one difference (I think) is that in q2-feature-classifier the min_coverage
parameter is about min coverage of the query; whereas in extract-seq-segments
this should be the min coverage of the reference, which is the shorter sequence in this case that is used to recruit additional sequences.