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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.
The text was updated successfully, but these errors were encountered:
The Problem
extract-seq-segments
does not have amin_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 themin_coverage
parameter is about min coverage of the query; whereas inextract-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.The text was updated successfully, but these errors were encountered: