ENH: `trim-alignment`, add `--p-addfragments` flag when using primer search option.
Closed this issue · 1 comments
mikerobeson commented
The trim-alignment action should use, by default (?), the --p-addfragments option. The reason is outlined in the help text for qiime alignment mafft-add:
--p-addfragments / --p-no-addfragments
Optimize for the addition of short sequence
fragments (for example, primer or amplicon
sequences). If not set, default sequence addition is
used.
mikerobeson commented
I had not noticed this earlier, but this option is already present here. 🤦♂️
Closing this non-issue.