ENH: Added ability to specify segment coverage value for extract-seq-segments.
#199
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nbokulich
requested changes
Aug 13, 2024
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Hey @mikerobeson looks good to me, I just have a minor comment inline. Thanks!
rescript/plugin_setup.py
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| @@ -1141,6 +1144,8 @@ | |||
| parameter_descriptions={ | |||
| 'threads': VSEARCH_PARAM_DESCRIPTIONS['threads'], | |||
| 'perc_identity': VSEARCH_PARAM_DESCRIPTIONS['perc_identity'], | |||
| 'target_coverage': 'Minimum coverage of reference segment ' | |||
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This param description is a little confusing. Could you please make it clearer?
Also since this is target_coverage, shouldn't this be the minimum coverage of the target, which is the reference sequence segments in this case? As written now it sounds like this is coverage of the input sequences.
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I've updated the help text to be more clear.
nbokulich
approved these changes
Aug 14, 2024
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Adresses #195
This PR adds the option
--p-target-coveragetoextract-seq-segments. This denotes the amount of coverage the sequence segments must have in order to extract the corresponding match from a longer sequence.