Restructuring

.clang-format

@@ -1,28 +1,29 @@
 # BasedOnStyle:  LLVM
 AccessModifierOffset: -3
 AlignAfterOpenBracket: Align
-AlignConsecutiveAssignments: false
+AlignConsecutiveAssignments: None
 # This would be nice to have but seems to also (mis)align function parameters
-AlignConsecutiveDeclarations: false
-AlignEscapedNewlinesLeft: true
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Left
 AlignOperands:   true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortBlocksOnASingleLine: false
+AllowShortBlocksOnASingleLine: Never
 AllowShortCaseLabelsOnASingleLine: true
+AllowShortEnumsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: Inline
-AllowShortIfStatementsOnASingleLine: true
-AllowShortLoopsOnASingleLine: true
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
 # This option is "deprecated and is retained for backwards compatibility."
 # AlwaysBreakAfterDefinitionReturnType: None
 AlwaysBreakAfterReturnType: None
 AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: true
+AlwaysBreakTemplateDeclarations: Yes
 BinPackArguments: true
 BinPackParameters: true
 BraceWrapping:
   AfterClass:      false
-  AfterControlStatement: false
+  AfterControlStatement: Never
   AfterEnum:       false
   AfterFunction:   true
   AfterNamespace:  false
@@ -32,33 +33,20 @@ BraceWrapping:
   BeforeCatch:     false
   BeforeElse:      false
   IndentBraces:    false
-BreakBeforeBinaryOperators: false
+BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Custom
 BreakBeforeTernaryOperators: true
 BreakConstructorInitializersBeforeComma: false
 ColumnLimit:     120
 CommentPragmas:  '^ IWYU pragma:'
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
 ConstructorInitializerIndentWidth: 3
 ContinuationIndentWidth: 3
 Cpp11BracedListStyle: true
 DerivePointerAlignment: false
 DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
 ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-IncludeCategories:
-  - Regex:           '^("|<)T'
-    Priority:        4
-  - Regex:           '^("|<)ROOT/'
-    Priority:        5
-  - Regex:           '^<.*\.h>'
-    Priority:        1
-  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
-    Priority:        2
-  - Regex:           '^(<|"(gtest|isl|json)/)'
-    Priority:        3
-  - Regex:           '.*'
-    Priority:        6
 IndentCaseLabels: false
 IndentWidth:     3
 IndentWrappedFunctionNames: false
@@ -75,12 +63,14 @@ PenaltyBreakComment: 300
 PenaltyBreakFirstLessLess: 120
 PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 60000
+PenaltyReturnTypeOnItsOwnLine: 10
 PointerAlignment: Right
-ReflowComments:  true
-SortIncludes: false
+ReflowComments: true
+SortIncludes: Never
 SpaceAfterCStyleCast: false
 SpaceBeforeAssignmentOperators: true
+# You want this : enable it if you have https://reviews.llvm.org/D32525
+# SpaceBeforeColon: false
 SpaceBeforeParens: ControlStatements
 SpaceInEmptyParentheses: false
 SpacesBeforeTrailingComments: 1
@@ -89,6 +79,24 @@ SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
-Standard:        Cpp11
+Standard:        c++17
 TabWidth:        3
 UseTab:          Never
+
+# Order alphabetically and by generality the included header files.
+IncludeCategories:
+  - Regex:           '^"[^/]+\"'
+    Priority:        10
+  - Regex:           '^("|<)T'
+    Priority:        12
+  - Regex:           '^"ROOT/'
+    Priority:        15
+  - Regex:           '^"cling/'
+    Priority:        20
+  - Regex:           '^"clang/'
+    Priority:        30
+  - Regex:           '^"llvm/'
+    Priority:        40
+  - Regex:           '^<'
+    Priority:        50
+

.clang-tidy

@@ -0,0 +1,76 @@
+Checks: >
+  -*,
+  bugprone-*,
+  clang-diagnostic-*,
+  clang-analyzer-*,
+  cppcoreguidelines-*,
+  llvm-*,
+  misc-*,
+  modernize-*,
+  performance-*,
+  portability-*,
+  readability-*,
+  -bugprone-narrowing-conversions,
+  -bugprone-easily-swappable-parameters,
+  -bugprone-implicit-widening-of-multiplication-result,
+  -bugprone-unchecked-optional-access,
+  -misc-const-correctness,
+  -misc-unused-parameters,
+  -misc-non-private-member-variables-in-classes,
+  -misc-no-recursion,
+  -misc-use-anonymous-namespace,
+  -modernize-return-braced-init-list,
+  -modernize-use-trailing-return-type,
+  -readability-braces-around-statements,
+  -readability-identifier-length,
+  -readability-magic-numbers,
+  -readability-named-parameter,
+  -readability-function-cognitive-complexity,
+  -readability-implicit-bool-conversion,
+  -cppcoreguidelines-avoid-magic-numbers,
+  -clang-analyzer-cplusplus.NewDeleteLeaks,
+
+CheckOptions:
+  - key:             readability-identifier-naming.ClassCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.FunctionCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.MemberCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.PrivateMemberPrefix
+    value:           'm_'
+  - key:             readability-identifier-naming.ProtectedMemberPrefix
+    value:           'm_'
+  - key:             readability-identifier-naming.PublicMemberPrefix
+    value:           ''
+  - key:             readability-identifier-naming.ParameterCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.UnionCase
+    value:           CamelCase
+  - key:             readability-identifier-naming.VariableCase
+    value:           aNy_CasE
+  - key:             readability-identifier-naming.IgnoreMainLikeFunctions
+    value:           1
+  - key:             readability-implicit-bool-conversion.AllowPointerConditions
+    value:           1
+  - key:             readability-magic-numbers.IgnorePowersOf2IntegerValues
+    value:           1
+  - key:             readability-magic-numbers.IgnoredIntegerValues
+    value:           4;8;16;
+  - key:             bugprone-argument-comment.CommentNullPtrs
+    value:           1
+  - key:             bugprone-argument-comment.CommentBoolLiterals
+    value:           1
+  - key:             bugprone-argument-comment.StrictMode
+    value:           1
+  - key:             bugprone-argument-comment.CommentIntegerLiterals
+    value:           1
+  - key:             bugprone-argument-comment.CommentUserDefinedLiterals
+    value:           1
+  - key:             bugprone-argument-comment.CommentStringLiterals
+    value:           1
+  - key:             bugprone-argument-comment.CommentFloatLiterals
+    value:           1
+  - key:             bugprone-argument-comment.CommentCharacterLiterals
+    value:           1
+

.gitignore

@@ -17,3 +17,12 @@ tmp/
 *.bk
 *.rootix
 *.sam
+build/
+cmake-build-*/
+Build/
+BUILD/
+Testing/
+.vscode/
+docs/html/
+docs/latex/
+html/

CMakeLists.txt

@@ -1,44 +1,65 @@
 cmake_minimum_required(VERSION 3.16)
+project(ramtools VERSION 1.0.0 LANGUAGES CXX)
 
-project(ramtools LANGUAGES CXX)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-find_package(ROOT 6.26 REQUIRED
-  COMPONENTS Core RIO Tree ROOTNTuple)
+option(RAMTOOLS_BUILD_TESTS "Build unit tests" ON)
+option(RAMTOOLS_BUILD_BENCHMARKS "Build benchmarks" ON)
+option(RAMTOOLS_BUILD_TOOLS "Build tools" ON)
 
-set(RNTUPLE_LIBS ROOT::ROOTNTuple ROOT::ROOTNTupleUtil)
+set(ROOT_MIN_VERSION 6.26)
+find_package(ROOT ${ROOT_MIN_VERSION} REQUIRED COMPONENTS Core RIO Tree ROOTNTuple ROOTNTupleUtil)
 
 include(${ROOT_USE_FILE})
 
-include_directories(${CMAKE_SOURCE_DIR} ${CMAKE_SOURCE_DIR}/rntuple)
+include(GNUInstallDirs)
+set(CMAKE_INSTALL_LIBDIR lib)
+set(CMAKE_INSTALL_INCLUDEDIR include)
 
-ROOT_STANDARD_LIBRARY_PACKAGE(ramrecord
-  SOURCES  ramrecord.C
-  HEADERS  ramrecord.h
-  LIBRARIES ROOT::Core ROOT::RIO ROOT::Tree
+    ROOT_STANDARD_LIBRARY_PACKAGE(ramcore
+    HEADERS
+        inc/ttree/RAMRecord.h
+        inc/ttree/Utils.h
+        inc/ttree/CigarOps.h
+        inc/rntuple/RAMNTupleRecord.h
+        inc/ramcore/SamParser.h
+        inc/ramcore/SamToTTree.h
+        inc/ramcore/SamToNTuple.h
+    SOURCES
+        src/ttree/RAMRecord.cxx
+        src/rntuple/RAMNTupleRecord.cxx
+        src/ramcore/SamParser.cxx
+        src/ramcore/SamToTTree.cxx
+        src/ramcore/SamToNTuple.cxx
+    LINKDEF
+        inc/ttree/LinkDef.h
+    DEPENDENCIES
+        ROOT::Core
+        ROOT::RIO
+        ROOT::Tree
+        ROOT::ROOTNTuple
+        ROOT::ROOTNTupleUtil
+    INSTALL_OPTIONS
+        DESTINATION ${CMAKE_INSTALL_LIBDIR}
 )
 
-set(RAMTOOLS_ROOT_LIBS ROOT::Core ROOT::RIO ROOT::Tree)
-
-ROOT_STANDARD_LIBRARY_PACKAGE(ramntuplerecord
-  SOURCES  rntuple/RAMntuplerecord.C
-  HEADERS  rntuple/RAMNTupleRecord.h
-  LIBRARIES ROOT::Core ROOT::RIO ROOT::Tree ${RNTUPLE_LIBS}
+target_include_directories(ramcore
+    PUBLIC
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/inc>
+        $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
 )
 
-ROOT_EXECUTABLE(samtoramntuple
-  rntuple/samtoramntuple.C
-  LIBRARIES ramntuplerecord ${RAMTOOLS_ROOT_LIBS} ${RNTUPLE_LIBS})
+install(DIRECTORY inc/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
-include(CTest)
-file(GLOB RAMTESTS tests/test_*.C)
-foreach(testfile ${RAMTESTS})
-  get_filename_component(testname ${testfile} NAME_WE)
-  add_test(NAME ${testname}
-           COMMAND root -l -b -q ${testfile}+)
-  set_tests_properties(${testname} PROPERTIES WORKING_DIRECTORY ${CMAKE_SOURCE_DIR})
-endforeach() 
+if(RAMTOOLS_BUILD_TOOLS)
+    add_subdirectory(tools)
+endif()
 
+if(RAMTOOLS_BUILD_TESTS)
+    enable_testing()
+    add_subdirectory(test)
+endif()