From 0084ef4355e3b9fa2e5b3e96633b37288cfb7be5 Mon Sep 17 00:00:00 2001
From: Daniel Olson <daniel.olson@me.com>
Date: Mon, 6 Oct 2025 07:34:16 -0600
Subject: [PATCH 1/4] Now adding debug symbols when building with debug

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

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f493aa6..9d4113d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -4,6 +4,8 @@ project(
         HOMEPAGE_URL https://github.com/TravisWheelerLab/ULTRA
 )
 
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g")
+
 # By default we do NOT build the standalone ULTRA library
 option(BUILD_ULTRA_LIB "Also build ULTRA as a standalone library" OFF)
 
diff --git a/src/ultra.hpp b/src/ultra.hpp
index fa924c2..0f4a26c 100644
--- a/src/ultra.hpp
+++ b/src/ultra.hpp
@@ -74,8 +74,7 @@ class Ultra {
 
   bool storeTraceAndSequence = false;
 
-  std::unordered_map<unsigned long long, std::vector<mregion> *>
-      masks_for_seq{};
+  std::unordered_map<unsigned long long, std::vector<mregion> *> masks_for_seq{};
   std::vector<RepeatRegion *> outRepeats{};
   std::vector<UModel *> models{};
 

From ce09da75096ff18600ec2adc99768cc3e8432461 Mon Sep 17 00:00:00 2001
From: Daniel Olson <daniel.olson@me.com>
Date: Mon, 6 Oct 2025 07:34:43 -0600
Subject: [PATCH 2/4] Changing the version number

---
 src/cli.hpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/cli.hpp b/src/cli.hpp
index 44ebbec..46a5b4b 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 "1.2.0"
+#define ULTRA_VERSION_STRING "1.2.1"
 #define DEBUG_STRING ""
 #ifdef DEBUG_PRAGMA
 #undef DEBUG_STRING

From 1ef2d4d572a0fa483b8d32634475b4fe28fcf320 Mon Sep 17 00:00:00 2001
From: Daniel Olson <daniel.olson@me.com>
Date: Mon, 6 Oct 2025 09:57:10 -0600
Subject: [PATCH 3/4] Changing logic of logo creation

---
 src/SequenceWindow.cpp | 6 ------
 src/repeat.cpp         | 4 +++-
 src/ultra.cpp          | 1 -
 3 files changed, 3 insertions(+), 8 deletions(-)

diff --git a/src/SequenceWindow.cpp b/src/SequenceWindow.cpp
index 5002fb0..2f31144 100644
--- a/src/SequenceWindow.cpp
+++ b/src/SequenceWindow.cpp
@@ -102,12 +102,6 @@ void SequenceWindow::CalculateSymbolFrequencies() {
   }
 }
 
-/*
-bool SequenceWindow::operator<(const SequenceWindow& rhs) {
-    if (this->seqID != rhs.seqID)
-        return this->seqID < rhs.readID;
-    return (this->readID < rhs.readID);
-}*/
 
 SequenceWindow::SequenceWindow(unsigned long ml, unsigned long mo) {
 
diff --git a/src/repeat.cpp b/src/repeat.cpp
index e1338c0..c57d291 100644
--- a/src/repeat.cpp
+++ b/src/repeat.cpp
@@ -54,7 +54,6 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
            }*/
 
     }
-
     else if (fdesc.type == CT_DELETION) {
       deletions += fdesc.indelNumber;
       bplace += fdesc.indelNumber;
@@ -77,6 +76,9 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
       i += bdesc.indelNumber;
     }
 
+    if (fplace > windowStart+repeatLength)
+      break;
+
     symbol s = window->seq[fplace];
     symbol sb = window->seq[bplace];
 
diff --git a/src/ultra.cpp b/src/ultra.cpp
index 335083b..10474d8 100644
--- a/src/ultra.cpp
+++ b/src/ultra.cpp
@@ -69,7 +69,6 @@ SequenceWindow *Ultra::GetSequenceWindow(SequenceWindow *seq, uthread *uth) {
     pthread_mutex_lock(&outerLock);
 
   // Check to see if we need to read more sequence first
-
   if (!reader->DoneReadingFile()) {
     if (!reader->IsReading()) {
       if (reader->ReadyWindowsSize() == 0) {

From 16b5afe522e1dccbd41af6bfb93222e67f320c64 Mon Sep 17 00:00:00 2001
From: Daniel Olson <daniel.olson@me.com>
Date: Mon, 6 Oct 2025 10:06:18 -0600
Subject: [PATCH 4/4] Changing logic of logo creation

---
 src/repeat.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/repeat.cpp b/src/repeat.cpp
index c57d291..a5013d7 100644
--- a/src/repeat.cpp
+++ b/src/repeat.cpp
@@ -76,7 +76,7 @@ void RepeatRegion::CreateLogo(SequenceWindow *window, UMatrix *matrix) {
       i += bdesc.indelNumber;
     }
 
-    if (fplace > windowStart+repeatLength)
+    if (fplace >= windowStart+repeatLength)
       break;
 
     symbol s = window->seq[fplace];