Adding static analysis setup

.clang-format

@@ -0,0 +1,12 @@
+BasedOnStyle: LLVM
+ColumnLimit: 80
+IndentWidth: 2
+AlwaysBreakAfterReturnType: All
+ContinuationIndentWidth: 2
+ConstructorInitializerIndentWidth: 2
+BraceWrapping:
+  BeforeElse: true
+  BeforeCatch: true
+BreakBeforeBraces: Custom
+BreakConstructorInitializers: AfterColon
+SpacesBeforeTrailingComments: 2

.clang-tidy

@@ -0,0 +1,31 @@
+Checks: 'cert-*,cppcoreguidelines-*,performance-*,clang-diagnostic-*,clang-analyzer-*,-clang-diagnostic-unqualified-std-cast-call,-clang-diagnostic-unknown-warning-option,-clang-analyzer-unix.BlockInCriticalSection,-cppcoreguidelines-pro-type-vararg'
+WarningsAsErrors: '*'
+HeaderFileExtensions:
+  - ''
+  - h
+  - hh
+  - hpp
+  - hxx
+ImplementationFileExtensions:
+  - c
+  - cc
+  - cpp
+  - cxx
+HeaderFilterRegex: ''
+ExcludeHeaderFilterRegex: 'OptionParser.hpp'
+FormatStyle: none
+CheckOptions:
+  cert-dcl16-c.NewSuffixes: 'L;LL;LU;LLU'
+  cert-err33-c.AllowCastToVoid: 'true'
+  cert-err33-c.CheckedFunctions: '::aligned_alloc;::asctime_s;::at_quick_exit;::atexit;::bsearch;::bsearch_s;::btowc;::c16rtomb;::c32rtomb;::calloc;::clock;::cnd_broadcast;::cnd_init;::cnd_signal;::cnd_timedwait;::cnd_wait;::ctime_s;::fclose;::fflush;::fgetc;::fgetpos;::fgets;::fgetwc;::fopen;::fopen_s;::fprintf;::fprintf_s;::fputc;::fputs;::fputwc;::fputws;::fread;::freopen;::freopen_s;::fscanf;::fscanf_s;::fseek;::fsetpos;::ftell;::fwprintf;::fwprintf_s;::fwrite;::fwscanf;::fwscanf_s;::getc;::getchar;::getenv;::getenv_s;::gets_s;::getwc;::getwchar;::gmtime;::gmtime_s;::localtime;::localtime_s;::malloc;::mbrtoc16;::mbrtoc32;::mbsrtowcs;::mbsrtowcs_s;::mbstowcs;::mbstowcs_s;::memchr;::mktime;::mtx_init;::mtx_lock;::mtx_timedlock;::mtx_trylock;::mtx_unlock;::printf_s;::putc;::putwc;::raise;::realloc;::remove;::rename;::scanf;::scanf_s;::setlocale;::setvbuf;::signal;::snprintf;::snprintf_s;::sprintf;::sprintf_s;::sscanf;::sscanf_s;::strchr;::strerror_s;::strftime;::strpbrk;::strrchr;::strstr;::strtod;::strtof;::strtoimax;::strtok;::strtok_s;::strtol;::strtold;::strtoll;::strtoul;::strtoull;::strtoumax;::strxfrm;::swprintf;::swprintf_s;::swscanf;::swscanf_s;::thrd_create;::thrd_detach;::thrd_join;::thrd_sleep;::time;::timespec_get;::tmpfile;::tmpfile_s;::tmpnam;::tmpnam_s;::tss_create;::tss_get;::tss_set;::ungetc;::ungetwc;::vfprintf;::vfprintf_s;::vfscanf;::vfscanf_s;::vfwprintf;::vfwprintf_s;::vfwscanf;::vfwscanf_s;::vprintf_s;::vscanf;::vscanf_s;::vsnprintf;::vsnprintf_s;::vsprintf;::vsprintf_s;::vsscanf;::vsscanf_s;::vswprintf;::vswprintf_s;::vswscanf;::vswscanf_s;::vwprintf_s;::vwscanf;::vwscanf_s;::wcrtomb;::wcschr;::wcsftime;::wcspbrk;::wcsrchr;::wcsrtombs;::wcsrtombs_s;::wcsstr;::wcstod;::wcstof;::wcstoimax;::wcstok;::wcstok_s;::wcstol;::wcstold;::wcstoll;::wcstombs;::wcstombs_s;::wcstoul;::wcstoull;::wcstoumax;::wcsxfrm;::wctob;::wctrans;::wctype;::wmemchr;::wprintf_s;::wscanf;::wscanf_s;'
+  cert-oop54-cpp.WarnOnlyIfThisHasSuspiciousField: 'false'
+  cert-str34-c.DiagnoseSignedUnsignedCharComparisons: 'false'
+  cppcoreguidelines-non-private-member-variables-in-classes.IgnorePublicMemberVariables: 'true'
+  google-readability-braces-around-statements.ShortStatementLines: '1'
+  google-readability-function-size.StatementThreshold: '800'
+  google-readability-namespace-comments.ShortNamespaceLines: '10'
+  google-readability-namespace-comments.SpacesBeforeComments: '2'
+  llvm-else-after-return.WarnOnConditionVariables: 'false'
+  llvm-else-after-return.WarnOnUnfixable: 'false'
+  llvm-qualified-auto.AddConstToQualified: 'false'
+SystemHeaders: 'false'

.cppcheck_suppress

@@ -0,0 +1,44 @@
+# MIT License
+#
+# Copyright (c) 2024 Andrew Smith
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+missingIncludeSystem
+constVariablePointer
+checkersReport
+unknownMacro
+unmatchedSuppression
+# Ignore unused function because it's too hard to get right
+unusedFunction
+# Ignore unused struct member because this won't go unnoticed anyway
+unusedStructMember
+# Ignore missing includes because if they are real things won't build
+missingInclude
+# Exclude external files
+*:*CLI11.hpp
+*:*json.hpp
+*:*asio*
+*:*smithlab_cpp*
+*:*ssl.hpp
+*:*indicators.hpp
+# Problem caused by external files
+toomanyconfigs
+# More problems caused by external files -- with too many ifdefs
+normalCheckLevelMaxBranches

CMakeLists.txt

@@ -0,0 +1,163 @@
+# This file is part of dnmtools
+#
+# Copyright (C) 2025 Andrew D. Smith
+#
+# Authors: Andrew D. Smith
+#
+# This is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This software is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+
+# to find the version of cmake do
+# $ cmake --version
+cmake_minimum_required(VERSION 3.28)
+project(
+  dnmtools
+  VERSION 1.4.4
+  DESCRIPTION
+  "Tools for analyzing DNA methylation data"
+  HOMEPAGE_URL https://github.com/smithlabcode/dnmtools
+  LANGUAGES CXX)
+
+# Set language version used
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED on)
+set(CMAKE_CXX_EXTENSIONS off)  # prevents std=gnu++17
+set(CMAKE_EXPORT_COMPILE_COMMANDS on)
+
+include(CheckIncludeFileCXX)
+include(CheckFunctionExists)
+include(CheckCXXCompilerFlag)
+
+include(GNUInstallDirs)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+
+configure_file(data/config.h.in config.h)
+
+# Collect any global linker options as needed and then apply them
+# individually to targets
+set(GLOBAL_COMPILE_OPTIONS "")
+set(GLOBAL_LINKER_OPTIONS "")
+
+if(USE_STATIC_LIBS)
+  # This needs to come before finding any libraries so that the static
+  # versions are identified
+  message(STATUS "Enabling static linkage for all non-system libraries")
+  message(STATUS "Configuring to clone ZLib")
+  include(ExternalProject)
+  set(ZLIB_CMAKE_ARGS
+    -DZLIB_BUILD_EXAMPLES=off
+    -DSKIP_INSTALL_FILES=on
+    -DCMAKE_POSITION_INDEPENDENT_CODE=on
+    -DCMAKE_INSTALL_PREFIX=${PROJECT_BINARY_DIR}/src/zlib
+    -DCMAKE_BUILD_TYPE=Release
+  )
+  if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+    list(APPEND ZLIB_CMAKE_ARGS
+      -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
+    )
+  endif()
+  ExternalProject_Add(
+    ZLIB
+    GIT_REPOSITORY https://github.com/madler/zlib.git
+    GIT_TAG master
+    CMAKE_ARGS ${ZLIB_CMAKE_ARGS}
+  )
+  # Include the built zlib headers and link against the built zlib library
+  set(ZLIB_INCLUDE_DIR "${PROJECT_BINARY_DIR}/src/zlib/include")
+  set(ZLIB_LIBRARY "${PROJECT_BINARY_DIR}/src/zlib/lib/libz.a")
+
+  # Create the CMake target for the built zlib
+  add_library(ZLIB_IMPORTED INTERFACE)
+  set_target_properties(ZLIB_IMPORTED PROPERTIES
+    INTERFACE_INCLUDE_DIRECTORIES ${ZLIB_INCLUDE_DIR}
+    INTERFACE_LINK_LIBRARIES ${ZLIB_LIBRARY}
+  )
+
+  # This alias means we don't need to worry where zlib came from
+  add_library(ZLIB::ZLIB ALIAS ZLIB_IMPORTED)
+
+  ExternalProject_Add(
+    HTSLIB
+    GIT_REPOSITORY https://github.com/samtools/htslib.git
+    GIT_TAG master
+    CONFIGURE_COMMAND ""
+    # "autoreconf -i <SOURCE_DIR>; <SOURCE_DIR>/configure"
+    BUILD_COMMAND make -C <SOURCE_DIR> lib-static -j
+    INSTALL_COMMAND ""
+    # make install
+    TEST_COMMAND ""
+    BUILD_BYPRODUCTS libhts.a
+  )
+  # ExternalProject_Add_Step(HTSLIB
+  #   bootstrap
+  #   COMMAND autoreconf -i <SOURCE_DIR>
+  #   DEPENDEES download
+  #   DEPENDERS configure
+  # )
+  ExternalProject_Get_Property(HTSLIB SOURCE_DIR)
+  message(STATUS "SOURCE_DIR: ${SOURCE_DIR}")
+
+  # Include the built zlib headers and link against the built zlib library
+  set(HTSLIB_INCLUDE_DIR "${SOURCE_DIR}/src/htslib/htslib")
+  set(HTSLIB_LIBRARY "${SOURCE_DIR}/htslib.a")
+
+  # Create the CMake target for the built zlib
+  add_library(HTSLIB_IMPORTED INTERFACE)
+  set_target_properties(HTSLIB_IMPORTED PROPERTIES
+    INTERFACE_INCLUDE_DIRECTORIES ${HTSLIB_INCLUDE_DIR}
+    INTERFACE_LINK_LIBRARIES ${HTSLIB_LIBRARY}
+  )
+  set_target_properties(HTSLIB_IMPORTED PROPERTIES IMPORTED_LOCATION ${HTSLIB_LIBRARY})
+
+  # This alias means we don't need to worry where htslib came from
+  add_library(HTSLIB::HTSLIB ALIAS HTSLIB_IMPORTED)
+
+  # Set static for the linker so the compiler's libraries will be static
+  ## ADS: using this instead of forcing -static for everything avoids the
+  ## static linkage that Aiso warns against, but also means it's not 100%
+  ## static linked ADS: can't do this if the compiler is AppleClang because
+  ## they don't have the libc++.a and the libgcc wouldn't make sense anyway.
+  if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")  # macOS
+    list(APPEND GLOBAL_LINKER_OPTIONS -static-libgcc -static-libstdc++)
+  endif()
+
+endif()
+
+if(ENABLE_LTO)
+  # Turn on LTO if we are building for distribution
+  include(CheckIPOSupported)
+  check_ipo_supported(RESULT result OUTPUT output)
+  if(result)
+    set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+  else()
+    message(FATAL_ERROR "IPO is not supported: ${output}")
+  endif()
+endif()
+
+if(STATIC_ANALYSIS)
+  include(cmake/static_analysis.cmake)
+endif()
+
+# ADS: set the most stringent warnings we can
+list(APPEND GLOBAL_COMPILE_OPTIONS
+  -Wall -Wextra -Wpedantic -Werror -Wfatal-errors
+)
+
+if(STRIP_PATHS_FROM_BINARIES)
+  # This is set if we have configured to distribute
+  set(PREFIX_MAP_ARG -ffile-prefix-map=)
+  list(TRANSFORM STRIP_SUB_LIST PREPEND ${PREFIX_MAP_ARG})
+  list(APPEND GLOBAL_COMPILE_OPTIONS ${STRIP_SUB_LIST})
+endif()
+
+message(STATUS "Finished global compile and linker configuration")
+
+add_subdirectory(src)

CPPLINT.cfg

@@ -0,0 +1,36 @@
+# MIT License
+#
+# Copyright (c) 2025 Andrew Smith
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+set noparent
+filter=-runtime/references
+filter=-build/include_subdir
+filter=-build/include_order
+filter=-build/c++11
+filter=-build/c++17
+# Formatting below handled by clang-format
+filter=-whitespace/line_length
+filter=-whitespace/newline
+filter=-readability/braces
+filter=-whitespace/semicolon
+filter=-whitespace/indent
+filter=-whitespace/braces
+filter=-whitespace/parens
+filter=-readability/nolint