From 66430bfc0b8d01735002ddde56f3a796f6acbcf4 Mon Sep 17 00:00:00 2001
From: Eli Levy Karin <eli.levy.karin@gmail.com>
Date: Fri, 19 Apr 2024 13:21:59 +0200
Subject: [PATCH] block the naughty mmseqs2 --add-orf-stop param

---
 src/commons/LocalParameters.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/commons/LocalParameters.h b/src/commons/LocalParameters.h
index 68e1076..b7d2065 100644
--- a/src/commons/LocalParameters.h
+++ b/src/commons/LocalParameters.h
@@ -103,6 +103,7 @@ class LocalParameters : public Parameters {
         predictexonsworkflow = combineList(searchworkflow, collectoptimalset);
         predictexonsworkflow.push_back(&PARAM_REVERSE_FRAGMENTS);
         predictexonsworkflow = removeParameter(predictexonsworkflow, PARAM_NUM_ITERATIONS);
+        predictexonsworkflow = removeParameter(predictexonsworkflow, PARAM_ADD_ORF_STOP);
 
         reduceredundancy.push_back(&PARAM_ALLOW_OVERLAP);
         reduceredundancy.push_back(&PARAM_THREADS);