Adding cmake stuff

.clang-format

@@ -1,24 +1,17 @@
-# MIT License
+# Copyright (C) 2025 Andrew D Smith
 #
-# Copyright (c) 2024 Andrew Smith
+# This program 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.
 #
-# 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:
+# This program 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.
 #
-# 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.
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <https://www.gnu.org/licenses/>.
 
 BasedOnStyle: LLVM
 ColumnLimit: 80

cmake/FindHTSLIB.cmake

@@ -0,0 +1,171 @@
+# SPDX-License-Identifier: GPL-3.0-or-later; (c) 2025 Andrew D Smith (author)
+#[=======================================================================[.rst:
+FindHTSLIB
+--------
+
+Find the native HTSLib includes and library. Based on the ZLIB module.
+
+#]=======================================================================]
+
+cmake_policy(PUSH)
+cmake_policy(SET CMP0159 NEW) # file(STRINGS) with REGEX updates CMAKE_MATCH_<n>
+
+if(HTSLIB_FIND_COMPONENTS AND NOT HTSLIB_FIND_QUIETLY)
+  message(AUTHOR_WARNING
+    "HTSLib does not provide any COMPONENTS.  Calling\n"
+    "  find_package(HTSLIB COMPONENTS ...)\n"
+    "will always fail."
+  )
+endif()
+
+set(_HTSLIB_SEARCHES)
+
+# Search HTSLIB_ROOT first if it is set.
+if(HTSLIB_ROOT)
+  set(_HTSLIB_SEARCH_ROOT PATHS ${HTSLIB_ROOT} NO_DEFAULT_PATH)
+  list(APPEND _HTSLIB_SEARCHES _HTSLIB_SEARCH_ROOT)
+endif()
+
+# Normal search.
+# Windows stuff
+set(_HTSLIB_x86 "(x86)")
+set(_HTSLIB_SEARCH_NORMAL
+  PATHS "$ENV{ProgramFiles}/htslib"
+  "$ENV{ProgramFiles${_HTSLIB_x86}}/htslib")
+unset(_HTSLIB_x86)
+list(APPEND _HTSLIB_SEARCHES _HTSLIB_SEARCH_NORMAL)
+
+if(HTSLIB_USE_STATIC_LIBS)
+  set(HTSLIB_NAMES hts)
+  set(HTSLIB_NAMES_DEBUG hts)
+else()
+  set(HTSLIB_NAMES hts)
+  set(HTSLIB_NAMES_DEBUG hts)
+endif()
+
+# Try each search configuration.
+foreach(search ${_HTSLIB_SEARCHES})
+  find_path(HTSLIB_INCLUDE_DIR NAMES htslib ${${search}} PATH_SUFFIXES include)
+endforeach()
+
+# Allow HTSLIB_LIBRARY to be set manually, as the location of the htslib library
+if(NOT HTSLIB_LIBRARY)
+  if(DEFINED CMAKE_FIND_LIBRARY_PREFIXES)
+    set(_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES "${CMAKE_FIND_LIBRARY_PREFIXES}")
+  else()
+    set(_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES)
+  endif()
+  if(DEFINED CMAKE_FIND_LIBRARY_SUFFIXES)
+    set(_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES "${CMAKE_FIND_LIBRARY_SUFFIXES}")
+  else()
+    set(_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES)
+  endif()
+  # Prefix/suffix of the win32/Makefile.gcc build
+  if(WIN32)
+    list(APPEND CMAKE_FIND_LIBRARY_PREFIXES "" "lib")
+    list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES ".dll.a")
+  endif()
+  # Support preference of static libs by adjusting CMAKE_FIND_LIBRARY_SUFFIXES
+  if(HTSLIB_USE_STATIC_LIBS)
+    if(WIN32)
+      set(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
+    else()
+      set(CMAKE_FIND_LIBRARY_SUFFIXES .a)
+    endif()
+  endif()
+
+  foreach(search ${_HTSLIB_SEARCHES})
+    find_library(HTSLIB_LIBRARY_RELEASE NAMES ${HTSLIB_NAMES} NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
+    find_library(HTSLIB_LIBRARY_DEBUG NAMES ${HTSLIB_NAMES_DEBUG} NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
+  endforeach()
+
+  # Restore the original find library ordering
+  if(DEFINED _htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES)
+    set(CMAKE_FIND_LIBRARY_SUFFIXES "${_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}")
+  else()
+    set(CMAKE_FIND_LIBRARY_SUFFIXES)
+  endif()
+  if(DEFINED _htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES)
+    set(CMAKE_FIND_LIBRARY_PREFIXES "${_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES}")
+  else()
+    set(CMAKE_FIND_LIBRARY_PREFIXES)
+  endif()
+
+  include(SelectLibraryConfigurations)
+  select_library_configurations(HTSLIB)
+endif()
+
+unset(HTSLIB_NAMES)
+unset(HTSLIB_NAMES_DEBUG)
+
+mark_as_advanced(HTSLIB_INCLUDE_DIR)
+
+if(HTSLIB_INCLUDE_DIR AND EXISTS "${HTSLIB_INCLUDE_DIR}/htslib/hts.h")
+  # Example: #define HTS_VERSION 101300
+  file(STRINGS "${HTSLIB_INCLUDE_DIR}/htslib/hts.h" HTSLIB_H_LIST REGEX "^#define HTS_VERSION")
+  list(GET HTSLIB_H_LIST 0 HTSLIB_H)  # Take the first matching line
+  if (HTSLIB_H MATCHES "#define[ \t]+HTS_VERSION[ \t]+\([0-9]+\)")
+    set(NUMERIC_VERSION "${CMAKE_MATCH_1}")
+    # Extract digits by position in string
+    # XYYYZZ => X = major, YYY = minor, ZZ = patch
+    string(SUBSTRING "${NUMERIC_VERSION}" 0 1 HTSLIB_VERSION_MAJOR)
+    string(SUBSTRING "${NUMERIC_VERSION}" 1 3 HTSLIB_VERSION_MINOR)
+    string(SUBSTRING "${NUMERIC_VERSION}" 4 2 HTSLIB_VERSION_PATCH)
+  else()
+    set(HTSLIB_VERSION_STRING "")
+    set(HTSLIB_VERSION_MAJOR "")
+    set(HTSLIB_VERSION_MINOR "")
+    set(HTSLIB_VERSION_PATCH "")
+  endif()
+  # Set canonical variables
+  set(HTSLIB_MAJOR_VERSION "${HTSLIB_VERSION_MAJOR}")
+  set(HTSLIB_MINOR_VERSION "${HTSLIB_VERSION_MINOR}")
+  set(HTSLIB_PATCH_VERSION "${HTSLIB_VERSION_PATCH}")
+  # Build the standard version string
+  set(HTSLIB_VERSION "${HTSLIB_VERSION_MAJOR}.${HTSLIB_VERSION_MINOR}")
+  # Only append patch if it's not "00"
+  if(NOT HTSLIB_VERSION_PATCH STREQUAL "00")
+    set(HTSLIB_VERSION "${HTSLIB_VERSION}.${HTSLIB_VERSION_PATCH}")
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(
+  HTSLIB
+  REQUIRED_VARS
+  HTSLIB_LIBRARY
+  HTSLIB_INCLUDE_DIR
+  VERSION_VAR
+  HTSLIB_VERSION
+  HANDLE_COMPONENTS
+)
+
+if(HTSLIB_FOUND)
+  set(HTSLIB_INCLUDE_DIRS ${HTSLIB_INCLUDE_DIR})
+  if(NOT HTSLIB_LIBRARIES)
+    set(HTSLIB_LIBRARIES ${HTSLIB_LIBRARY})
+  endif()
+  if(NOT TARGET HTSLIB::HTSLIB)
+    add_library(HTSLIB::HTSLIB UNKNOWN IMPORTED)
+    set_target_properties(HTSLIB::HTSLIB PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES "${HTSLIB_INCLUDE_DIRS}")
+    if(HTSLIB_LIBRARY_RELEASE)
+      set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
+        IMPORTED_CONFIGURATIONS RELEASE)
+      set_target_properties(HTSLIB::HTSLIB PROPERTIES
+        IMPORTED_LOCATION_RELEASE "${HTSLIB_LIBRARY_RELEASE}")
+    endif()
+    if(HTSLIB_LIBRARY_DEBUG)
+      set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
+        IMPORTED_CONFIGURATIONS DEBUG)
+      set_target_properties(HTSLIB::HTSLIB PROPERTIES
+        IMPORTED_LOCATION_DEBUG "${HTSLIB_LIBRARY_DEBUG}")
+    endif()
+    if(NOT HTSLIB_LIBRARY_RELEASE AND NOT HTSLIB_LIBRARY_DEBUG)
+      set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
+        IMPORTED_LOCATION "${HTSLIB_LIBRARY}")
+    endif()
+  endif()
+endif()
+
+cmake_policy(POP)

src/AbismalAlign.hpp

@@ -39,18 +39,22 @@ typedef std::vector<std::uint32_t> bam_cigar_t;
 static inline score_t
 count_deletions(const bam_cigar_t &cigar) {
   score_t ans = 0;
+  // cppcheck-suppress-begin useStlAlgorithm
   for (const auto &x : cigar)
     if (abismal_bam_cigar_op(x) == ABISMAL_BAM_CDEL)
       ans += abismal_bam_cigar_oplen(x);
+  // cppcheck-suppress-end useStlAlgorithm
   return ans;
 }
 
 static inline score_t
 count_insertions(const bam_cigar_t &cigar) {
   score_t ans = 0;
+  // cppcheck-suppress-begin useStlAlgorithm
   for (const auto &x : cigar)
     if (abismal_bam_cigar_op(x) == ABISMAL_BAM_CINS)
       ans += abismal_bam_cigar_oplen(x);
+  // cppcheck-suppress-end useStlAlgorithm
   return ans;
 }