done with this

Author: SamStan4

.vscode/settings.json

@@ -55,7 +55,8 @@
     "xmemory": "cpp",
     "xstring": "cpp",
     "xtr1common": "cpp",
-    "xutility": "cpp"
+    "xutility": "cpp",
+    "sstream": "cpp"
   },
   "C_Cpp_Runner.msvcBatchPath": "C:/Program Files/Microsoft Visual Studio/2022/Community/VC/Auxiliary/Build/vcvarsall.bat",
   "C_Cpp_Runner.cCompilerPath": "gcc",

bin/app

@@ -30,4 +30,20 @@ run-sample: $(TARGET)
 	else \
 		echo "Error: Executable $(TARGET) not found. Please build it first."; \
 		exit 1; \
+	fi
+
+run-brca2: $(TARGET)
+	@if [ -f $(TARGET) ]; then \
+		./$(TARGET) input/Human-Mouse-BRCA2-cds.fasta; \
+	else \
+		echo "Error: Executable $(TARGET) not found. Please build it first."; \
+		exit 1; \
+	fi
+
+run-blind: $(TARGET)
+	@if [ -f $(TARGET) ]; then \
+		./$(TARGET) input/Opsin1_colorblindness_gene.fasta; \
+	else \
+		echo "Error: Executable $(TARGET) not found. Please build it first."; \
+		exit 1; \
 	fi

makefile

@@ -23,6 +23,8 @@ void program_wrapper::run_program(const int arg_count, const char* const* arg_ve
   if (!io_utils::load_two_genes(arg_vector[1], gene_one, gene_two, gene_one_name, gene_two_name)) {
     throw std::runtime_error("error, not able to load genes from file");
   }
-  int64_t result = alignment::execute_modified_global_alignment(gene_one, gene_two);
-  std::cout << result << std::endl;
+  int64_t result1 = alignment::execute_global_alignment(gene_one, gene_two);
+  int32_t result2 = alignment::execute_modified_global_alignment(gene_one, gene_two);
+  std::cout << result1 << std::endl;
+  std::cout << result2 << std::endl;
 }