ENH: adds --p-[no-]keep-primers option to trim-alignment.
#214
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…on region On branch update-align-trim Changes to be committed: modified: rescript/plugin_setup.py new file: rescript/tests/data/small-silva-v4-trim-keeplength-nokeepprimers.fasta modified: rescript/tests/test_trim_alignment.py modified: rescript/trim_alignment.py
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Attempts to fix #213 by allowing the user to toggle the
--p-keep-primer-location/--p-no-keep-primer-locationparameter. The--p-no-keep-primer-locationoption is the default. This option will not return an alignment containing the primer positions within the extracted output. If the user would like to retain the primer positions within the extracted alignment output then the user can specify--p-keep-primer-location.