1.0.2b

CMakeLists.txt

@@ -10,6 +10,9 @@ if (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE STREQUAL "")
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 endif()
 
+if(NOT CMAKE_BUILD_TYPE STREQUAL "Release")
+    add_definitions(-DDEBUG_PRAGMA=1)
+endif()
 
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)

src/cli.cpp

@@ -63,7 +63,7 @@ void Settings::prepare_settings() {
       ->group("Output");
 
   app.add_option("--max_consensus", this->max_consensus_period,
-               "The maximum length of consensus pattern to include in output")
+                 "The maximum length of consensus pattern to include in output")
       ->default_val(this->max_consensus_period)
       ->group("Output");
 
@@ -626,21 +626,25 @@ void Settings::assign_settings() {
 
     // Small models use less than 160 mb per thread
     else if (period_memory <= 200000) {
-      this->window_size = 400 * this->max_period;
+      this->window_size = 1000 * this->max_period;
     }
 
     // medium models use less than 1 GB per thread
     else if (period_memory <= 2000000) {
-      this->window_size = 100 * this->max_period;
+      this->window_size = 500 * this->max_period;
     }
 
     // medium models use less than 1 GB per thread
-    else if (period_memory <= 4000000) {
+    else if (period_memory <= 20000000) {
+      this->window_size = 100 * this->max_period;
+    }
+
+    else if (period_memory <= 50000000) {
       this->window_size = 50 * this->max_period;
     }
 
     // Large models use less than 4 GB per thread
-    else {
+    else  {
       this->window_size = 25 * this->max_period;
     }
 

src/cli.hpp

@@ -5,7 +5,13 @@
 #ifndef ULTRA_CLI_HPP
 #define ULTRA_CLI_HPP
 
-#define ULTRA_VERSION_STRING "1.0.2"
+#define ULTRA_VERSION_STRING "1.0.2b"
+#define DEBUG_STRING ""
+#ifdef DEBUG_PRAGMA
+#undef DEBUG_STRING
+#define DEBUG_STRING " **WARNING** BUILT WITHOUT RELEASE OPTIMIZATION **WARNING** \n"
+#endif
+
 
 
 #include "../lib/CLI11.hpp"
@@ -109,6 +115,7 @@ struct Settings {
                "(U)ltra (L)ocates (T)andemly (R)epetitive (A)reas\n"
                "     Daniel R. Olson and Travis J. Wheeler\n"
                "                 Version " ULTRA_VERSION_STRING "\n"
+               DEBUG_STRING
                "     Use '--cite' for citation instructions\n"
                "=================================================\n"};