style(hmnrandomread): super-linter, clang-format

guillaume-gricourt · Jan 10, 2023 · 72ffe39 · 72ffe39
1 parent 72e7f06
commit 72ffe39
Show file tree

Hide file tree

Showing 33 changed files with 1,985 additions and 1,870 deletions.
diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,166 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Right
+AlignOperands:   Align
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: Never
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  BeforeLambdaBody: false
+  BeforeWhile:     false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeConceptDeclarations: true
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+StatementAttributeLikeMacros:
+  - Q_EMIT
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '.*'
+    Priority:        1
+    SortPriority:    0
+    CaseSensitive:   false
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+IndentRequires:  false
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Right
+ReflowComments:  true
+SortIncludes:    true
+SortJavaStaticImport: Before
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        Latest
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseCRLF:         false
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - STRINGIZE
+  - PP_STRINGIZE
+  - BOOST_PP_STRINGIZE
+  - NS_SWIFT_NAME
+  - CF_SWIFT_NAME
+...
+
diff --git a/include/args.hpp b/include/args.hpp
@@ -12,62 +12,62 @@
 
 class Args {
 private:
-    std::string soft_name;
-    std::vector<std::unique_ptr<Reference>> references;
-    int mean_insert_size = 500;
-    int std_insert_size = 50;
-    int length_reads = 150;
-    bool usage_visible = false;
-    std::string read1 = "";
-    std::string read2 = "";
-    long long int seed = 0;
+  std::string soft_name;
+  std::vector<std::unique_ptr<Reference>> references;
+  int mean_insert_size = 500;
+  int std_insert_size = 50;
+  int length_reads = 150;
+  bool usage_visible = false;
+  std::string read1 = "";
+  std::string read2 = "";
+  long long int seed = 0;
 
-    std::string profile_error_id = "";
+  std::string profile_error_id = "";
 
-    std::shared_ptr<ProfileDiversity> profile_diversity = nullptr;
-    std::shared_ptr<ProfileError> profile_error = nullptr;
+  std::shared_ptr<ProfileDiversity> profile_diversity = nullptr;
+  std::shared_ptr<ProfileError> profile_error = nullptr;
 
 public:
-    Args(std::string);
-    ~Args() = default;
+  Args(std::string);
+  ~Args() = default;
 
-    // Getters Setters
-    int getNbReads() const noexcept;
-    int getMeanInsertSize() const noexcept;
-    int getStdInsertSize() const noexcept;
-    int getLengthReads() const noexcept;
-    bool getUsageVisible() const noexcept;
-    std::string getRead1() const noexcept;
-    std::string getRead2() const noexcept;
-    std::string getProfileErrorId() const noexcept;
-    long long int getSeed() const noexcept;
+  // Getters Setters
+  int getNbReads() const noexcept;
+  int getMeanInsertSize() const noexcept;
+  int getStdInsertSize() const noexcept;
+  int getLengthReads() const noexcept;
+  bool getUsageVisible() const noexcept;
+  std::string getRead1() const noexcept;
+  std::string getRead2() const noexcept;
+  std::string getProfileErrorId() const noexcept;
+  long long int getSeed() const noexcept;
 
-    std::shared_ptr<ProfileError> getProfileError() noexcept;
-    std::shared_ptr<ProfileDiversity> getProfileDiversity() noexcept;
+  std::shared_ptr<ProfileError> getProfileError() noexcept;
+  std::shared_ptr<ProfileDiversity> getProfileDiversity() noexcept;
 
-    void setNbReads(const std::string);
-    void setMeanInsertSize(const std::string);
-    void setStdInsertSize(const std::string);
-    void setLengthReads(const std::string);
-    void setRead1(const std::string &);
-    void setRead2(const std::string &);
-    void setSeed(const std::string &);
+  void setNbReads(const std::string);
+  void setMeanInsertSize(const std::string);
+  void setStdInsertSize(const std::string);
+  void setLengthReads(const std::string);
+  void setRead1(const std::string &);
+  void setRead2(const std::string &);
+  void setSeed(const std::string &);
 
-    void setProfileDiversity(const std::string &n);
-    void setProfileError(const std::string &n);
-    void setProfileErrorId(const std::string &n);
+  void setProfileDiversity(const std::string &n);
+  void setProfileError(const std::string &n);
+  void setProfileErrorId(const std::string &n);
 
-    // Intermediary
-    std::vector<std::unique_ptr<Reference>> *getReferences() noexcept;
-    int addReference(std::string);
-    bool isValid() const noexcept;
-    bool isOutputPaired() const noexcept;
-    bool isProfileError() const noexcept;
-    bool isProfileDiversity() const noexcept;
-    void removeReferences(int);
+  // Intermediary
+  std::vector<std::unique_ptr<Reference>> *getReferences() noexcept;
+  int addReference(std::string);
+  bool isValid() const noexcept;
+  bool isOutputPaired() const noexcept;
+  bool isProfileError() const noexcept;
+  bool isProfileDiversity() const noexcept;
+  void removeReferences(int);
 
-    // Others
-    void showUsage(const std::string);
-    void showVersion(const std::string) const;
+  // Others
+  void showUsage(const std::string);
+  void showVersion(const std::string) const;
 };
-#endif  // INCLUDE_ARGS_HPP_
+#endif // INCLUDE_ARGS_HPP_
diff --git a/include/diversity.hpp b/include/diversity.hpp
@@ -4,21 +4,21 @@
 
 class Diversity {
 private:
-    double mut_rate;
-    double indel_frac;
-    double indel_extend;
-    int max_ins_size;
+  double mut_rate;
+  double indel_frac;
+  double indel_extend;
+  int max_ins_size;
 
 public:
-    double getMutRate() const noexcept;
-    double getIndelFrac() const noexcept;
-    double getIndelExtend() const noexcept;
-    int getMaxInsSize() const noexcept;
+  double getMutRate() const noexcept;
+  double getIndelFrac() const noexcept;
+  double getIndelExtend() const noexcept;
+  int getMaxInsSize() const noexcept;
 
-    void setMutRate(double);
-    void setIndelFrac(double);
-    void setIndelExtend(double);
-    void setMaxInsSize(double);
+  void setMutRate(double);
+  void setIndelFrac(double);
+  void setIndelExtend(double);
+  void setMaxInsSize(double);
 };
 
-#endif  // INCLUDE_DIVERSITY_HPP_
+#endif // INCLUDE_DIVERSITY_HPP_
diff --git a/include/faidxh.hpp b/include/faidxh.hpp
@@ -6,24 +6,24 @@
 
 class Faidx {
 private:
-    std::string name;
-    long long int len;
-    long long int seq_offset;
-    int line_blen;
-    int line_len;
-    int qual_offset;
+  std::string name;
+  long long int len;
+  long long int seq_offset;
+  int line_blen;
+  int line_len;
+  int qual_offset;
 
 public:
-    Faidx();
-    Faidx(std::string, long long int, long long int, int, int, int);
+  Faidx();
+  Faidx(std::string, long long int, long long int, int, int, int);
 
-    // inherit
-    std::string getName() const noexcept;
-    int getLineLen() const noexcept;
-    int getLineBlen() const noexcept;
-    long long int getLen() const noexcept;
-    long long int getSeqOffset() const noexcept;
-    int getQualOffset() const noexcept;
+  // inherit
+  std::string getName() const noexcept;
+  int getLineLen() const noexcept;
+  int getLineBlen() const noexcept;
+  long long int getLen() const noexcept;
+  long long int getSeqOffset() const noexcept;
+  int getQualOffset() const noexcept;
 };
 
-#endif  // INLUDE_FAIDXH_HPP_
+#endif // INLUDE_FAIDXH_HPP_