From 35d83f6c598b9c22745e029b5bbd3108acbf2261 Mon Sep 17 00:00:00 2001
From: KatharinaHoff <katharina.hoff@gmail.com>
Date: Fri, 22 Dec 2023 15:27:08 +0100
Subject: [PATCH] addressing issue
 https://github.com/Gaius-Augustus/BRAKER/issues/635

---
 scripts/braker.pl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/braker.pl b/scripts/braker.pl
index e047476..7c8b142 100755
--- a/scripts/braker.pl
+++ b/scripts/braker.pl
@@ -768,7 +768,7 @@
     exit(0);
 }
 
-if( $soft_off ) {
+if( $soft_off == 1 ) {
     $soft_mask = 0;
 }
 
@@ -3293,8 +3293,8 @@ sub check_options {
             = "\# "
             . (localtime)
             . ": ERROR: in file " . __FILE__ ." at line ". __LINE__ ."\n"
-            . "--UTR=on has been set but --softmasking has not been enabled. "
-            . "A softmasked genome file and the option --softmasking and a "
+            . "--UTR=on has been set and --softmasking_off has been enabled. "
+            . "A softmasked genome file and the not the option --softmask_off and a "
             . "bam file must be provided in order to run --UTR=on (in contrast "
             . "to other modes, where a hints file can replace the alignment "
             . "file, the bam file is strictly required for UTR training).\n";