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Merge pull request #42 from bcgsc/nthash2
Nthash2
2 parents 941f99f + a81cc75 commit 13e63fa

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‎.clang-format‎

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---
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Language: Cpp
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# BasedOnStyle: Mozilla
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AccessModifierOffset: -2
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AlignAfterOpenBracket: Align
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AlignArrayOfStructures: None
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AlignConsecutiveMacros: None
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AlignConsecutiveAssignments: None
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AlignConsecutiveBitFields: None
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AlignConsecutiveDeclarations: None
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AlignEscapedNewlines: Right
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AlignOperands: Align
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AlignTrailingComments: true
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AllowAllArgumentsOnNextLine: true
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AllowAllConstructorInitializersOnNextLine: true
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AllowAllParametersOfDeclarationOnNextLine: false
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AllowShortEnumsOnASingleLine: true
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AllowShortBlocksOnASingleLine: Never
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AllowShortCaseLabelsOnASingleLine: false
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AllowShortFunctionsOnASingleLine: Inline
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AllowShortLambdasOnASingleLine: All
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AllowShortIfStatementsOnASingleLine: Never
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AllowShortLoopsOnASingleLine: false
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AlwaysBreakAfterDefinitionReturnType: TopLevel
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AlwaysBreakAfterReturnType: TopLevel
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AlwaysBreakBeforeMultilineStrings: false
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AlwaysBreakTemplateDeclarations: Yes
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AttributeMacros:
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- __capability
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BinPackArguments: false
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BinPackParameters: false
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BraceWrapping:
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AfterCaseLabel: false
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AfterClass: true
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AfterControlStatement: Never
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AfterEnum: true
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AfterFunction: true
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AfterNamespace: false
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AfterObjCDeclaration: false
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AfterStruct: true
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AfterUnion: true
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AfterExternBlock: true
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BeforeCatch: false
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BeforeElse: false
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BeforeLambdaBody: false
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BeforeWhile: false
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IndentBraces: false
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SplitEmptyFunction: false
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SplitEmptyRecord: false
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SplitEmptyNamespace: true
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BreakBeforeBinaryOperators: None
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BreakBeforeConceptDeclarations: true
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BreakBeforeBraces: Custom
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BreakBeforeInheritanceComma: false
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BreakInheritanceList: BeforeComma
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BreakBeforeTernaryOperators: true
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BreakConstructorInitializersBeforeComma: false
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BreakConstructorInitializers: BeforeComma
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BreakAfterJavaFieldAnnotations: false
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BreakStringLiterals: true
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ColumnLimit: 80
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CommentPragmas: '^ IWYU pragma:'
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CompactNamespaces: false
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ConstructorInitializerAllOnOneLineOrOnePerLine: false
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ConstructorInitializerIndentWidth: 2
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ContinuationIndentWidth: 2
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Cpp11BracedListStyle: false
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DeriveLineEnding: true
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DerivePointerAlignment: false
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DisableFormat: false
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EmptyLineAfterAccessModifier: Never
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EmptyLineBeforeAccessModifier: LogicalBlock
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ExperimentalAutoDetectBinPacking: false
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FixNamespaceComments: false
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ForEachMacros:
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- foreach
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- Q_FOREACH
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- BOOST_FOREACH
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IfMacros:
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- KJ_IF_MAYBE
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IncludeBlocks: Preserve
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IncludeCategories:
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- Regex: '^"(llvm|llvm-c|clang|clang-c)/'
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Priority: 2
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SortPriority: 0
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CaseSensitive: false
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- Regex: '^(<|"(gtest|gmock|isl|json)/)'
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Priority: 3
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SortPriority: 0
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CaseSensitive: false
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- Regex: '.*'
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Priority: 1
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SortPriority: 0
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CaseSensitive: false
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IncludeIsMainRegex: '(Test)?$'
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IncludeIsMainSourceRegex: ''
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IndentAccessModifiers: false
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IndentCaseLabels: true
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IndentCaseBlocks: false
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IndentGotoLabels: true
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IndentPPDirectives: None
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IndentExternBlock: AfterExternBlock
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IndentRequires: false
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IndentWidth: 2
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IndentWrappedFunctionNames: false
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InsertTrailingCommas: None
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JavaScriptQuotes: Leave
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JavaScriptWrapImports: true
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KeepEmptyLinesAtTheStartOfBlocks: true
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LambdaBodyIndentation: Signature
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MacroBlockBegin: ''
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MacroBlockEnd: ''
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MaxEmptyLinesToKeep: 1
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NamespaceIndentation: None
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ObjCBinPackProtocolList: Auto
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ObjCBlockIndentWidth: 2
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ObjCBreakBeforeNestedBlockParam: true
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ObjCSpaceAfterProperty: true
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ObjCSpaceBeforeProtocolList: false
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PenaltyBreakAssignment: 2
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PenaltyBreakBeforeFirstCallParameter: 19
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PenaltyBreakComment: 300
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PenaltyBreakFirstLessLess: 120
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PenaltyBreakString: 1000
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PenaltyBreakTemplateDeclaration: 10
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PenaltyExcessCharacter: 1000000
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PenaltyReturnTypeOnItsOwnLine: 200
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PenaltyIndentedWhitespace: 0
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PointerAlignment: Left
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PPIndentWidth: -1
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ReferenceAlignment: Pointer
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ReflowComments: true
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ShortNamespaceLines: 1
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SortIncludes: CaseSensitive
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SortJavaStaticImport: Before
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SortUsingDeclarations: true
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SpaceAfterCStyleCast: false
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SpaceAfterLogicalNot: false
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SpaceAfterTemplateKeyword: false
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SpaceBeforeAssignmentOperators: true
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SpaceBeforeCaseColon: false
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SpaceBeforeCpp11BracedList: false
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SpaceBeforeCtorInitializerColon: true
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SpaceBeforeInheritanceColon: true
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SpaceBeforeParens: ControlStatements
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SpaceAroundPointerQualifiers: Default
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SpaceBeforeRangeBasedForLoopColon: true
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SpaceInEmptyBlock: false
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SpaceInEmptyParentheses: false
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SpacesBeforeTrailingComments: 1
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SpacesInAngles: Never
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SpacesInConditionalStatement: false
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SpacesInContainerLiterals: true
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SpacesInCStyleCastParentheses: false
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SpacesInLineCommentPrefix:
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Minimum: 1
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Maximum: -1
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SpacesInParentheses: false
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SpacesInSquareBrackets: false
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SpaceBeforeSquareBrackets: false
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BitFieldColonSpacing: Both
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Standard: Latest
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StatementAttributeLikeMacros:
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- Q_EMIT
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StatementMacros:
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- Q_UNUSED
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- QT_REQUIRE_VERSION
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TabWidth: 8
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UseCRLF: false
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UseTab: Never
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WhitespaceSensitiveMacros:
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- STRINGIZE
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- PP_STRINGIZE
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- BOOST_PP_STRINGIZE
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- NS_SWIFT_NAME
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- CF_SWIFT_NAME
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...

‎.clang-tidy‎

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{
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Checks: '*,
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-cppcoreguidelines-pro-bounds-array-to-pointer-decay,
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-hicpp-no-array-decay,
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-fuchsia-default-arguments,
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-fuchsia-overloaded-operator,
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-cppcoreguidelines-pro-bounds-pointer-arithmetic,
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-hicpp-avoid-c-arrays,-google-readability-casting,
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-cppcoreguidelines-pro-bounds-constant-array-index,
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-modernize-avoid-c-arrays,
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-cppcoreguidelines-avoid-c-arrays,
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-modernize-use-equals-default,
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-hicpp-use-equals-default,
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-google-runtime-references,
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-google-explicit-constructor,
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-hicpp-explicit-conversions,
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-misc-non-private-member-variables-in-classes,
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-cppcoreguidelines-special-member-functions,
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-modernize-use-nodiscard,
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-hicpp-special-member-functions,
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-llvm-header-guard,
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-google-runtime-int,
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-readability-isolate-declaration,
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-fuchsia-default-arguments-calls,
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-modernize-use-trailing-return-type,
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-bugprone-branch-clone,
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-fuchsia-default-arguments-declarations,
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-cppcoreguidelines-pro-type-union-access,
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-cppcoreguidelines-pro-type-cstyle-cast,
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-cppcoreguidelines-pro-type-vararg,
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-android-cloexec-pipe,
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-hicpp-signed-bitwise,
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-cert-err58-cpp,
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-hicpp-vararg,-abseil-string-find-startswith,
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-misc-definitions-in-headers,
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-clang-analyzer-valist.Uninitialized,
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-android-cloexec-open,
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-cppcoreguidelines-owning-memory,
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-cppcoreguidelines-non-private-member-variables-in-classes,
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-fuchsia-statically-constructed-objects,
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-modernize-return-braced-init-list,
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-clang-analyzer-unix.Vfork,
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-clang-analyzer-security.insecureAPI.vfork,
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-cppcoreguidelines-init-variables,
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readability-identifier-naming,
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-google-readability-todo,
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-cppcoreguidelines-macro-usage,
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-cppcoreguidelines-pro-type-reinterpret-cast,
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-llvmlibc-*,
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-readability-function-cognitive-complexity,
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-altera-struct-pack-align,
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-bugprone-easily-swappable-parameters,
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-altera-unroll-loops,
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-altera-id-dependent-backward-branch,
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-clang-diagnostic-unused-command-line-argument,
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-clang-diagnostic-unneeded-internal-declaration',
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WarningsAsErrors: '*',
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CheckOptions: [
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{ key: readability-identifier-naming.ClassCase, value: CamelCase },
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{ key: readability-identifier-naming.VariableCase, value: lower_case },
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{ key: readability-identifier-naming.FunctionCase, value: lower_case },
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{ key: readability-identifier-naming.ParameterCase, value: lower_case },
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{ key: readability-identifier-naming.StaticConstantCase, value: lower_case },
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{ key: readability-identifier-naming.GlobalConstantCase, value: UPPER_CASE },
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{ key: readability-identifier-naming.GlobalConstantPointerCase, value: UPPER_CASE },
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{ key: readability-identifier-naming.ConstexprVariableCase, value: UPPER_CASE },
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]
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}

‎.gitignore‎

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bin/
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lib/
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build/
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release/
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cmake-build-debug/
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# IntelliJ project files
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.idea
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*.iml
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out
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gen
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### C++
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# Prerequisites
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*.d
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# Compiled Object files
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*.slo
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*.lo
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*.o
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*.obj
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# Precompiled Headers
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*.gch
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*.pch
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# Compiled Dynamic libraries
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*.so
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*.dylib
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*.dll
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# Fortran module files
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*.mod
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*.smod
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# Compiled Static libraries
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*.lai
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*.la
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*.a
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*.lib
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# Executables
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*.exe
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*.out
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*.app
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### CMake
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CMakeLists.txt.user
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CMakeCache.txt
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CMakeFiles
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CMakeScripts
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Testing
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Makefile
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cmake_install.cmake
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install_manifest.txt
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compile_commands.json
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CTestTestfile.cmake
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_deps

‎.gitmodules‎

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[submodule "vendor/argparse"]
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path = vendor/argparse
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url = git@github.com:p-ranav/argparse.git
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[submodule "vendor/btllib"]
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path = vendor/btllib
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url = git@github.com:bcgsc/btllib.git

‎CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.22)
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project(ntHash)
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set(CMAKE_CXX_STANDARD 17)
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if (NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE Release)
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endif ()
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set(CMAKE_CXX_FLAGS "-Wall -Wextra")
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set(CMAKE_CXX_FLAGS_DEBUG "-g")
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set(CMAKE_CXX_FLAGS_RELEASE "-O3")
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include_directories(include)
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include_directories(vendor/btllib/include)
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include_directories(vendor/argparse/include)
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file(GLOB SRC_FILES ${PROJECT_SOURCE_DIR}/src/nthash/*.cpp)
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add_custom_command(
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OUTPUT ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a
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COMMAND ${PROJECT_SOURCE_DIR}/vendor/btllib/compile --prefix ${PROJECT_BINARY_DIR}/btllib
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)
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add_library(nthash_lib STATIC ${SRC_FILES})
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set_target_properties(nthash_lib PROPERTIES OUTPUT_NAME "nthash")
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add_executable(nthash main.cpp ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
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target_link_libraries(nthash ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
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target_link_libraries(nthash ${PROJECT_BINARY_DIR}/libnthash.a)
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add_executable(nthash_tests ${PROJECT_SOURCE_DIR}/tests/tests.cpp ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
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target_link_libraries(nthash_tests ${PROJECT_BINARY_DIR}/btllib/lib/libbtllib.a)
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target_link_libraries(nthash_tests ${PROJECT_BINARY_DIR}/libnthash.a)
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enable_testing()
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add_test(NAME nthash_tests COMMAND $<TARGET_FILE:nthash_tests>)

‎ChangeLog‎

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