Description: fix failure to invoke vsearch --search_exact
Author: Étienne Mollier <etienne.mollier@mailoo.org>
Forwarded: https://github.com/qiime2/q2-feature-classifier/pull/170
Last-Update: 2021-01-27
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- q2-feature-classifier.orig/q2_feature_classifier/_vsearch.py
+++ q2-feature-classifier/q2_feature_classifier/_vsearch.py
@@ -50,6 +50,11 @@
            '--threads', str(threads)]
     if search_exact:
         cmd[1] = '--search_exact'
+        # These options are not compatible with a --search_exact command.
+        for pop_arg in ['--id', '--maxaccepts', '--maxrejects', '--query_cov']:
+            pop_idx = cmd.index(pop_arg)
+            cmd.pop(pop_idx)
+            cmd.pop(pop_idx)
     if top_hits_only:
         cmd.append('--top_hits_only')
     if output_no_hits: