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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:
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