From 540e8dd1c355054430bcff817dd85eeb7e901989 Mon Sep 17 00:00:00 2001
From: Daniel Olson <olson@ebi.ac.uk>
Date: Fri, 28 Aug 2026 10:58:05 +0100
Subject: [PATCH] Fixing -s bug (it was not being used previously)

---
 src/cli.hpp   | 2 +-
 src/ultra.cpp | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/cli.hpp b/src/cli.hpp
index 46a5b4b..cfffe78 100644
--- a/src/cli.hpp
+++ b/src/cli.hpp
@@ -5,7 +5,7 @@
 #ifndef ULTRA_CLI_HPP
 #define ULTRA_CLI_HPP
 
-#define ULTRA_VERSION_STRING "1.2.1"
+#define ULTRA_VERSION_STRING "1.2.2"
 #define DEBUG_STRING ""
 #ifdef DEBUG_PRAGMA
 #undef DEBUG_STRING
diff --git a/src/ultra.cpp b/src/ultra.cpp
index 10474d8..4e1b4da 100644
--- a/src/ultra.cpp
+++ b/src/ultra.cpp
@@ -326,7 +326,8 @@ void Ultra::OutputRepeats(bool flush) {
     }
 
     r->SortConsensi();
-    if (r->repeatLength / r->repeatPeriod >= settings->min_units)
+    if (r->regionScore >= scoreThreshold &&
+        r->repeatLength / r->repeatPeriod >= settings->min_units)
       OutputRepeat(r);
 
     delete r;