.clang-format in the git repo

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+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlinesLeft: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: true
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBinaryOperators: false
+BreakBeforeBraces: Linux
+BreakBeforeTernaryOperators: false
+BreakConstructorInitializersBeforeComma: false
+ColumnLimit: 120
+CommentPragmas: ''
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 0
+ContinuationIndentWidth: 0
+Cpp11BracedListStyle: true
+DerivePointerBinding: false
+IndentCaseLabels: false
+IndentFunctionDeclarationAfterType: true
+IndentWidth: 4
+Language: Cpp
+MaxEmptyLinesToKeep: 3
+NamespaceIndentation: All
+ObjCSpaceAfterProperty: true
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakBeforeFirstCallParameter: 120
+PenaltyBreakComment: 120
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 100
+PenaltyExcessCharacter: 1
+PenaltyReturnTypeOnItsOwnLine: 20
+PointerBindsToType: true
+ReflowComments: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpacesBeforeTrailingComments: 4
+SpaceInEmptyParentheses: false
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+Standard: Cpp11
+TabWidth: 4
+UseTab: Never
\ No newline at end of file

-.clang-format
+EditMe
 rna1999.dG
 .vscode/*
 

-# Please set the following variables to the correct paths for JAR3D:
-jar3dexec="/home/persalteas/Software/jar3dbin/jar3d_2014-12-11.jar"
-ILmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/IL/3.2/lib"
-HLmotifDir="/home/persalteas/Data/RNA/motifs/Matlab_results/HL/3.2/lib"
-CPLEXDir="/opt/ibm/ILOG/CPLEX_Studio_Community128"
-IEIGEN="/usr/local/include/eigen3"