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12 files changed

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-317
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‎.vscode/c_cpp_properties.json‎

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{
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"configurations": [
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{
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"name": "windows-gcc-x64",
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"includePath": [
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"${workspaceFolder}/**"
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],
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"compilerPath": "gcc",
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"cStandard": "${default}",
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"cppStandard": "${default}",
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"intelliSenseMode": "windows-gcc-x64",
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"compilerArgs": [
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""
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]
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}
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],
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"version": 4
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}

‎.vscode/launch.json‎

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{
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Debug C++ Project (WSL)",
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"type": "cppdbg",
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"request": "launch",
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"program": "${workspaceFolder}/bin/app_debug",
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"args": [
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"input/base-sample.fasta"
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],
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"stopAtEntry": false,
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"cwd": "${workspaceFolder}",
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"environment": [],
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"externalConsole": false,
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"MIMode": "gdb",
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"setupCommands": [
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{
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"description": "Enable pretty-printing for gdb",
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"text": "-enable-pretty-printing",
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"ignoreFailures": true
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}
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],
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"miDebuggerPath": "/usr/bin/gdb"
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},
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{
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"name": "C/C++ Runner: Debug Session",
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"type": "cppdbg",
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"request": "launch",
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"args": [],
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"stopAtEntry": false,
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"externalConsole": true,
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"cwd": "c:/Users/samue/Desktop/Pairwise-Sequence-Alignment-Algorithm/src/alignment",
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"program": "c:/Users/samue/Desktop/Pairwise-Sequence-Alignment-Algorithm/src/alignment/build/Debug/outDebug",
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"MIMode": "gdb",
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"miDebuggerPath": "gdb",
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"setupCommands": [
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{
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"description": "Enable pretty-printing for gdb",
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"text": "-enable-pretty-printing",
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"ignoreFailures": true
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}
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]
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}
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]
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}

‎.vscode/settings.json‎

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{
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"files.associations": {
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"algorithm": "cpp",
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"atomic": "cpp",
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"bit": "cpp",
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"cctype": "cpp",
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"charconv": "cpp",
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"clocale": "cpp",
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"cmath": "cpp",
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"compare": "cpp",
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"concepts": "cpp",
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"cstddef": "cpp",
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"cstdint": "cpp",
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"cstdio": "cpp",
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"cstdlib": "cpp",
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"cstring": "cpp",
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"ctime": "cpp",
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"cwchar": "cpp",
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"exception": "cpp",
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"format": "cpp",
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"fstream": "cpp",
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"initializer_list": "cpp",
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"ios": "cpp",
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"iosfwd": "cpp",
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"iostream": "cpp",
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"istream": "cpp",
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"iterator": "cpp",
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"limits": "cpp",
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"list": "cpp",
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"locale": "cpp",
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"memory": "cpp",
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"new": "cpp",
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"optional": "cpp",
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"ostream": "cpp",
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"stdexcept": "cpp",
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"streambuf": "cpp",
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"string": "cpp",
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"system_error": "cpp",
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"tuple": "cpp",
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"type_traits": "cpp",
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"typeinfo": "cpp",
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"unordered_set": "cpp",
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"utility": "cpp",
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"vector": "cpp",
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"xfacet": "cpp",
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"xhash": "cpp",
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"xiosbase": "cpp",
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"xlocale": "cpp",
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"xlocbuf": "cpp",
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"xlocinfo": "cpp",
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"xlocmes": "cpp",
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"xlocmon": "cpp",
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"xlocnum": "cpp",
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"xloctime": "cpp",
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"xmemory": "cpp",
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"xstring": "cpp",
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"xtr1common": "cpp",
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"xutility": "cpp"
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}
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{
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"files.associations": {
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"algorithm": "cpp",
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"atomic": "cpp",
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"bit": "cpp",
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"cctype": "cpp",
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"charconv": "cpp",
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"clocale": "cpp",
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"cmath": "cpp",
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"compare": "cpp",
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"concepts": "cpp",
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"cstddef": "cpp",
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"cstdint": "cpp",
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"cstdio": "cpp",
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"cstdlib": "cpp",
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"cstring": "cpp",
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"ctime": "cpp",
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"cwchar": "cpp",
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"exception": "cpp",
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"format": "cpp",
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"fstream": "cpp",
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"initializer_list": "cpp",
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"ios": "cpp",
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"iosfwd": "cpp",
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"iostream": "cpp",
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"istream": "cpp",
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"iterator": "cpp",
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"limits": "cpp",
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"list": "cpp",
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"locale": "cpp",
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"memory": "cpp",
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"new": "cpp",
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"optional": "cpp",
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"ostream": "cpp",
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"stdexcept": "cpp",
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"streambuf": "cpp",
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"string": "cpp",
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"system_error": "cpp",
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"tuple": "cpp",
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"type_traits": "cpp",
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"typeinfo": "cpp",
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"unordered_set": "cpp",
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"utility": "cpp",
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"vector": "cpp",
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"xfacet": "cpp",
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"xhash": "cpp",
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"xiosbase": "cpp",
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"xlocale": "cpp",
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"xlocbuf": "cpp",
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"xlocinfo": "cpp",
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"xlocmes": "cpp",
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"xlocmon": "cpp",
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"xlocnum": "cpp",
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"xloctime": "cpp",
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"xmemory": "cpp",
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"xstring": "cpp",
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"xtr1common": "cpp",
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"xutility": "cpp"
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},
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"C_Cpp_Runner.msvcBatchPath": "C:/Program Files/Microsoft Visual Studio/2022/Community/VC/Auxiliary/Build/vcvarsall.bat",
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"C_Cpp_Runner.cCompilerPath": "gcc",
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"C_Cpp_Runner.cppCompilerPath": "g++",
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"C_Cpp_Runner.debuggerPath": "gdb",
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"C_Cpp_Runner.cStandard": "",
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"C_Cpp_Runner.warnings": [
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"-Wall",
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"-Wextra",
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"-Wpedantic",
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"-Wshadow",
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"-Wformat=2",
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"-Wcast-align",
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"-Wconversion",
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"-Wsign-conversion",
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"-Wnull-dereference"
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],
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"C_Cpp_Runner.msvcWarnings": [
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"/W4",
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"/permissive-",
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"/w14242",
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"/w14287",
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"/w14296",
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"/w14311",
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"/w14826",
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"/w44062",
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"/w44242",
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"/w14905",
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"/w14906",
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"/w14263",
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"/w44265",
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"/w14928"
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],
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"C_Cpp_Runner.enableWarnings": true,
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"C_Cpp_Runner.warningsAsError": false,
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"C_Cpp_Runner.compilerArgs": [],
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"C_Cpp_Runner.linkerArgs": [],
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"C_Cpp_Runner.includePaths": [],
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"C_Cpp_Runner.includeSearch": [
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"*",
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"**/*"
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],
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"C_Cpp_Runner.excludeSearch": [
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"**/build",
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"**/build/**",
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"**/.*",
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"**/.*/**",
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"**/.vscode",
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"**/.vscode/**"
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],
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"C_Cpp_Runner.useAddressSanitizer": false,
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"C_Cpp_Runner.useUndefinedSanitizer": false,
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"C_Cpp_Runner.useLeakSanitizer": false,
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"C_Cpp_Runner.showCompilationTime": false,
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"C_Cpp_Runner.useLinkTimeOptimization": false,
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"C_Cpp_Runner.msvcSecureNoWarnings": false
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}

‎.vscode/tasks.json‎

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{
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"version": "2.0.0",
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"tasks": [
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{
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"label": "build-debug",
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"type": "shell",
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"command": "make debug",
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"group": {
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"kind": "build",
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"isDefault": true
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},
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"problemMatcher": ["$gcc"]
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}
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]
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}

‎bin/app‎

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‎obj/alignment/alignment.o‎

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‎obj/alignment/de_cell.o‎

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‎output.txt‎

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‎src/alignment/alignment.cpp‎

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#include "./alignment.hpp"
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namespace alignment {
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int64_t execute_global_alignment(const std::string& string_one, const std::string& string_two) {
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const size_t row_size = string_one.size() + 1;
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const size_t col_size = string_two.size() + 1;
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std::vector<dp_cell> cur_dp_row(col_size, dp_cell());
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std::vector<dp_cell> prev_dp_row(col_size, dp_cell());
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// temp
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std::ofstream s("./output.txt");
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// prev_dp_row[0].print_scores(s);
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// s << " ";
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for (size_t i = 1; i < col_size; ++i) {
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prev_dp_row[i].set_top_row(i);
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// prev_dp_row[i].print_scores(s);
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// s << " ";
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int64_t execute_global_alignment_bad(const std::string& string_one, const std::string& string_two) {
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if (string_one.empty() || string_two.empty()) {
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return 0;
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}
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size_t max_row = string_one.size();
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size_t max_col = string_one.size();
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std::vector<std::vector<dp_cell>> dp_table(max_row, std::vector<dp_cell>(max_col, dp_cell()));
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for (size_t row_idx = 1; row_idx < row_size; ++row_idx) {
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cur_dp_row[0].set_left_col(row_idx);
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// cur_dp_row[0].print_scores(s);
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// s << " ";
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for (size_t col_idx = 1; col_idx < col_size; ++col_idx) {
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cur_dp_row[col_idx].score_cell(
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prev_dp_row[col_idx-1],
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prev_dp_row[col_idx],
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cur_dp_row[col_idx-1],
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string_one[row_idx-1],
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string_two[col_idx-1]
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);
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// cur_dp_row[col_idx].print_scores(s);
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// s << " ";
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for (size_t i = 1; i < max_row; ++i) {
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for (size_t j = 1; j < max_col; ++i) {
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}
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// s << std::endl;
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std::swap(prev_dp_row, cur_dp_row);
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}
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s << prev_dp_row.back().to_string() << std::endl;
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s.close();
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return prev_dp_row.back().get_max_score();
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}
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// int32_t execute_modified_global_alignment(const std::string& string_one, const std::string& string_two) {

‎src/alignment/alignment.hpp‎

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#include "./dp_cell.hpp"
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namespace alignment {
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int64_t execute_global_alignment(const std::string&, const std::string&);
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int64_t execute_global_alignment_bad(const std::string&, const std::string&);
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// int32_t execute_modified_global_alignment(const std::string&, const std::string&);
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}
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