attractivechaos · KOLANICH · Aug 18, 2021 · Aug 18, 2021 · Aug 18, 2021 · Aug 18, 2021
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,17 @@
+[submodule "cmake/thirdParty/Boilerplate"]
+	path = cmake/thirdParty/Boilerplate
+	url = https://github.com/KOLANICH-libs/Boilerplate.cmake
+	branch = master
+	shallow = true
+
+[submodule "cmake/thirdParty/DoxygenUtils"]
+	path = cmake/thirdParty/DoxygenUtils
+	url = https://github.com/KOLANICH-libs/DoxygenUtils.cmake
+	branch = master
+	shallow = true
+
+[submodule "cmake/thirdParty/DetectDependentHeaders"]
+	path = cmake/thirdParty/DetectDependentHeaders
+	url = https://github.com/KOLANICH-libs/DetectDependentHeaders.cmake
+	branch = master
+	shallow = true
diff --git a/C/CMakeLists.txt b/C/CMakeLists.txt
@@ -0,0 +1,9 @@
+add_subdirectory("include")
+
+set(C_SUBLIBS "knetfile;bgzf;kalloc;keigen;kexpr;khmm;kmath;knhx;kson;kstring;ksw;kthread;kurl;kopen;ksa")  # order matters!
+
+foreach(C_SUBLIB ${C_SUBLIBS})
+	add_subdirectory("${C_SUBLIB}")
+endforeach()
+
+pass_through_cpack_vars()
diff --git a/C/bgzf/CMakeLists.txt b/C/bgzf/CMakeLists.txt
@@ -0,0 +1,30 @@
+buildAndPackageLib("bzgf"
+	COMPONENT "bzgf"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nSomething related to compression."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
+
+option(BGZF_WITH_CACHE "Enable caching in bzgf" ON)
+if(BGZF_WITH_CACHE)
+	target_compile_definitions(bzgf PRIVATE "-DBGZF_CACHE") #khash is header-only
+	target_link_libraries(bzgf PRIVATE "${PROJECT_NAME}")
+endif()
+
+option(BGZF_WITH_KNETFILE "Use knetfile in bzgf" OFF)
+if(BGZF_WITH_KNETFILE)
+	target_compile_definitions(bzgf PRIVATE "-D_USE_KNETFILE")
+	target_link_libraries(bzgf PRIVATE knetfile)
+	set(CPACK_COMPONENT_BGZF_DEPENDS "${CPACK_COMPONENT_BGZF_DEPENDS};knetfile")
+
+	list(APPEND CPACK_DEBIAN_BZGF_PACKAGE_DEPENDS "${CPACK_DEBIAN_KNETFILE_PACKAGE_NAME}")
+	string(REPLACE ";" ", " CPACK_DEBIAN_BZGF_PACKAGE_DEPENDS "${CPACK_DEBIAN_BZGF_PACKAGE_DEPENDS}")
+	set(CPACK_DEBIAN_BZGF_PACKAGE_DEPENDS "${CPACK_DEBIAN_BZGF_PACKAGE_DEPENDS}" PARENT_SCOPE)
+
+	list(APPEND CPACK_RPM_BZGF_PACKAGE_DEPENDS "${CPACK_RPM_KNETFILE_PACKAGE_NAME}")
+	string(REPLACE ";" ", " CPACK_RPM_BZGF_PACKAGE_DEPENDS "${CPACK_RPM_BZGF_PACKAGE_DEPENDS}")
+	set(CPACK_RPM_BZGF_PACKAGE_DEPENDS "${CPACK_RPM_BZGF_PACKAGE_DEPENDS}" PARENT_SCOPE)
+
+	pass_through_cpack_vars()
+endif()
diff --git a/bgzf.c → C/bgzf/bgzf.c b/bgzf.c → C/bgzf/bgzf.c
diff --git a/bgzf.h → C/bgzf/bgzf.h b/bgzf.h → C/bgzf/bgzf.h
diff --git a/C/include/CMakeLists.txt b/C/include/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("${PROJECT_NAME}"
+	COMPONENT "headers"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nHeader-only libraries"
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kavl-lite.h → C/include/kavl-lite.h b/kavl-lite.h → C/include/kavl-lite.h
diff --git a/kavl.h → C/include/kavl.h b/kavl.h → C/include/kavl.h
diff --git a/kbit.h → C/include/kbit.h b/kbit.h → C/include/kbit.h
diff --git a/kbtree.h → C/include/kbtree.h b/kbtree.h → C/include/kbtree.h
diff --git a/kdq.h → C/include/kdq.h b/kdq.h → C/include/kdq.h
diff --git a/ketopt.h → C/include/ketopt.h b/ketopt.h → C/include/ketopt.h
diff --git a/kgraph.h → C/include/kgraph.h b/kgraph.h → C/include/kgraph.h
diff --git a/khash.h → C/include/khash.h b/khash.h → C/include/khash.h
diff --git a/khashl.h → C/include/khashl.h b/khashl.h → C/include/khashl.h
diff --git a/klist.h → C/include/klist.h b/klist.h → C/include/klist.h
diff --git a/krmq.h → C/include/krmq.h b/krmq.h → C/include/krmq.h
diff --git a/krng.h → C/include/krng.h b/krng.h → C/include/krng.h
diff --git a/kseq.h → C/include/kseq.h b/kseq.h → C/include/kseq.h
diff --git a/ksort.h → C/include/ksort.h b/ksort.h → C/include/ksort.h
diff --git a/kvec.h → C/include/kvec.h b/kvec.h → C/include/kvec.h
diff --git a/C/kalloc/CMakeLists.txt b/C/kalloc/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("kalloc"
+	COMPONENT "kalloc"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nAn allocator of memory"
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kalloc.c → C/kalloc/kalloc.c b/kalloc.c → C/kalloc/kalloc.c
diff --git a/kalloc.h → C/kalloc/kalloc.h b/kalloc.h → C/kalloc/kalloc.h
diff --git a/C/keigen/CMakeLists.txt b/C/keigen/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("keigen"
+	COMPONENT "keigen"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nAn eigensolver"
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/keigen.c → C/keigen/keigen.c b/keigen.c → C/keigen/keigen.c
diff --git a/keigen.h → C/keigen/keigen.h b/keigen.h → C/keigen/keigen.h
diff --git a/C/kexpr/CMakeLists.txt b/C/kexpr/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("kexpr"
+	COMPONENT "keigen"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA small rudimentary scripting language for arythmetic expressions"
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kexpr.c → C/kexpr/kexpr.c b/kexpr.c → C/kexpr/kexpr.c
diff --git a/kexpr.h → C/kexpr/kexpr.h b/kexpr.h → C/kexpr/kexpr.h
diff --git a/C/khmm/CMakeLists.txt b/C/khmm/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("khmm"
+	COMPONENT "khmm"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA basic HMM library."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/khmm.c → C/khmm/khmm.c b/khmm.c → C/khmm/khmm.c
diff --git a/khmm.h → C/khmm/khmm.h b/khmm.h → C/khmm/khmm.h
diff --git a/C/kmath/CMakeLists.txt b/C/kmath/CMakeLists.txt
@@ -0,0 +1,12 @@
+buildAndPackageLib("kmath"
+	COMPONENT "kmath"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA numerical routines including MT19937-64 pseudorandom generator, basic nonlinear programming and a few special math functions."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
+
+if(MSVC)
+else()
+	target_link_libraries(kmath PUBLIC m)
+endif()
diff --git a/kmath.c → C/kmath/kmath.c b/kmath.c → C/kmath/kmath.c
diff --git a/kmath.h → C/kmath/kmath.h b/kmath.h → C/kmath/kmath.h
diff --git a/C/knetfile/CMakeLists.txt b/C/knetfile/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("knetfile"
+	COMPONENT "knetfile"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nRandom access to remote files on HTTP or FTP."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/knetfile.c → C/knetfile/knetfile.c b/knetfile.c → C/knetfile/knetfile.c
diff --git a/knetfile.h → C/knetfile/knetfile.h b/knetfile.h → C/knetfile/knetfile.h
diff --git a/C/knhx/CMakeLists.txt b/C/knhx/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("knhx"
+	COMPONENT "knhx"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nNewick tree format parser."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/knhx.c → C/knhx/knhx.c b/knhx.c → C/knhx/knhx.c
diff --git a/knhx.h → C/knhx/knhx.h b/knhx.h → C/knhx/knhx.h
diff --git a/C/kopen/CMakeLists.txt b/C/kopen/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("kopen"
+	COMPONENT "kopen"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA library for smart stream, files and sockets opening."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kopen.c → C/kopen/kopen.c b/kopen.c → C/kopen/kopen.c
@@ -12,6 +12,9 @@
 #include <arpa/inet.h>
 #include <sys/socket.h>
 #endif
+#ifdef _POSIX_VERSION
+#include <sys/wait.h>
+#endif
 
 #ifdef _WIN32
 #define _KO_NO_NET

diff --git a/C/kopen/kopen.h b/C/kopen/kopen.h
@@ -0,0 +1,4 @@
+#pragma once
+
+int kclose(void *a);
+void *kopen(char const *fn, int *_fd);
diff --git a/C/ksa/CMakeLists.txt b/C/ksa/CMakeLists.txt
@@ -0,0 +1,19 @@
+set(DESCR "Constructs suffix arrays for strings with multiple sentinels, based on a revised SAIS algorithm.")
+
+buildAndPackageLib("ksa32"
+	COMPONENT "ksa32"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\n${DESCR}\n\nUses 32-bit integers."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}/ksa32.h"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
+
+buildAndPackageLib("ksa64"
+	COMPONENT "ksa64"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\n${DESCR}\n\nUses 64-bit integers."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}/ksa64.h"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
+
+target_compile_definitions(ksa64 PRIVATE "-D_KSA64")
diff --git a/ksa.c → C/ksa/ksa.c b/ksa.c → C/ksa/ksa.c
diff --git a/C/ksa/ksa32.h b/C/ksa/ksa32.h
@@ -0,0 +1,30 @@
+#pragma once
+
+int ksa_bwt(unsigned char *T, int n, int k);
+
+/**
+ * Recursively construct the suffix array for a string containing multiple
+ * sentinels. NULL is taken as the sentinel.
+ *
+ * @param T   NULL terminated input string (there can be multiple NULLs)
+ * @param SA  output suffix array
+ * @param fs  working space available in SA (typically 0 when first called)
+ * @param n   length of T, including the trailing NULL
+ * @param k   size of the alphabet (typically 256 when first called)
+ * @param cs  # bytes per element in T; 1 or sizeof(saint_t) (typically 1 when first called)
+ *
+ * @return    0 upon success
+ */
+int ksa_core(unsigned char const *T, int *SA, int fs, int n, int k, int cs);
+
+/**
+ * Construct the suffix array for a NULL terminated string possibly containing
+ * multiple sentinels (NULLs).
+ *
+ * @param T[0..n-1]  NULL terminated input string
+ * @param SA[0..n-1] output suffix array
+ * @param n          length of the given string, including NULL
+ * @param k          size of the alphabet including the sentinel; no more than 256
+ * @return           0 upon success
+ */
+int ksa_sa(unsigned char const *T, int *SA, int n, int k);
diff --git a/C/ksa/ksa64.h b/C/ksa/ksa64.h
@@ -0,0 +1,30 @@
+#pragma once
+
+int ksa_bwt64(unsigned char *T, long int n, int k);
+
+/**
+ * Recursively construct the suffix array for a string containing multiple
+ * sentinels. NULL is taken as the sentinel.
+ *
+ * @param T   NULL terminated input string (there can be multiple NULLs)
+ * @param SA  output suffix array
+ * @param fs  working space available in SA (typically 0 when first called)
+ * @param n   length of T, including the trailing NULL
+ * @param k   size of the alphabet (typically 256 when first called)
+ * @param cs  # bytes per element in T; 1 or sizeof(saint_t) (typically 1 when first called)
+ *
+ * @return    0 upon success
+ */
+int ksa_core64(unsigned char const *T, long int *SA, long int fs, long int n, long int k, int cs);
+
+/**
+ * Construct the suffix array for a NULL terminated string possibly containing
+ * multiple sentinels (NULLs).
+ *
+ * @param T[0..n-1]  NULL terminated input string
+ * @param SA[0..n-1] output suffix array
+ * @param n          length of the given string, including NULL
+ * @param k          size of the alphabet including the sentinel; no more than 256
+ * @return           0 upon success
+ */
+int ksa_sa64(unsigned char const *T, long int *SA, long int n, int k);
diff --git a/C/kson/CMakeLists.txt b/C/kson/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("kson"
+	COMPONENT "kson"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA small and lightweight JSON parser."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kson.c → C/kson/kson.c b/kson.c → C/kson/kson.c
diff --git a/kson.h → C/kson/kson.h b/kson.h → C/kson/kson.h
diff --git a/C/kstring/CMakeLists.txt b/C/kstring/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("kstring"
+	COMPONENT "kstring"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nA basic string library."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/kstring.c → C/kstring/kstring.c b/kstring.c → C/kstring/kstring.c
diff --git a/kstring.h → C/kstring/kstring.h b/kstring.h → C/kstring/kstring.h
diff --git a/C/ksw/CMakeLists.txt b/C/ksw/CMakeLists.txt
@@ -0,0 +1,7 @@
+buildAndPackageLib("ksw"
+	COMPONENT "ksw"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nStriped Smith-Waterman algorithm."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+)
diff --git a/ksw.c → C/ksw/ksw.c b/ksw.c → C/ksw/ksw.c
diff --git a/ksw.h → C/ksw/ksw.h b/ksw.h → C/ksw/ksw.h
diff --git a/C/kthread/CMakeLists.txt b/C/kthread/CMakeLists.txt
@@ -0,0 +1,11 @@
+find_package(Threads REQUIRED)
+
+set(CPACK_DEBIAN_KTHREAD_PACKAGE_SHLIBDEPS ON)
+buildAndPackageLib("kthread"
+	COMPONENT "kthread"
+	DESCRIPTION "${PROJECT_DESCRIPTION}\n\nSimple threading models."
+	CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+	PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+	INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+	PRIVATE_LIBS "Threads::Threads"
+)
diff --git a/kthread.c → C/kthread/kthread.c b/kthread.c → C/kthread/kthread.c
diff --git a/kthread.h → C/kthread/kthread.h b/kthread.h → C/kthread/kthread.h
diff --git a/C/kurl/CMakeLists.txt b/C/kurl/CMakeLists.txt
@@ -0,0 +1,14 @@
+find_package(CURL)
+
+if(CURL_FOUND)
+	set(CPACK_DEBIAN_KURL_PACKAGE_SHLIBDEPS ON)
+	buildAndPackageLib("kurl"
+		COMPONENT "kurl"
+		DESCRIPTION "${PROJECT_DESCRIPTION}\n\nSomething like knetfile, but implemented above cURL."
+		CMAKE_EXPORT_NAMESPACE "${PROJECT_NAME}"
+		PUBLIC_INCLUDES "${CMAKE_CURRENT_LIST_DIR}"
+		INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME}"
+		PRIVATE_LIBS "CURL::libcurl"
+		#PKG_CONFIG_REQUIRES "libcurl"
+	)
+endif()
diff --git a/kurl.c → C/kurl/kurl.c b/kurl.c → C/kurl/kurl.c
diff --git a/kurl.h → C/kurl/kurl.h b/kurl.h → C/kurl/kurl.h
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,83 @@
+cmake_minimum_required(VERSION 3.7.2)
+
+set(CMAKE_USE_RELATIVE_PATHS TRUE)
+project("klib")
+set("PROJECT_DESCRIPTION" "A standalone and lightweight C library that strives for efficiency and a small memory footprint, some of which components are among the most efficient
+implementations of similar algorithms or data structures in all programming languages, in terms of both speed and memory use.")
+set("PROJECT_HOMEPAGE_URL" "https://github.com/attractivechaos/klib")
+
+set(CPACK_PACKAGE_VENDOR "klib developers")
+set(CPACK_PACKAGE_VERSION_MAJOR "0")
+set(CPACK_PACKAGE_VERSION_MINOR "0")
+set(CPACK_PACKAGE_VERSION_PATCH "0")
+set(CPACK_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+
+set(OUR_CMAKE_MODULES_DIR "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+set(OUR_CMAKE_3PARTY_MODULES_DIR "${OUR_CMAKE_MODULES_DIR}/thirdParty")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${OUR_CMAKE_MODULES_DIR}" "${OUR_CMAKE_3PARTY_MODULES_DIR}" "${OUR_CMAKE_3PARTY_MODULES_DIR}/Boilerplate" "${OUR_CMAKE_3PARTY_MODULES_DIR}/DetectDependentHeaders" "${OUR_CMAKE_3PARTY_MODULES_DIR}/DoxygenUtils")
+
+
+include(Boilerplate)
+include(DetectDependentHeaders)
+include(DoxygenUtils)
+
+set(CPACK_DEBIAN_ENABLE_COMPONENT_DEPENDS ON)
+set(CPACK_RPM_ENABLE_COMPONENT_DEPENDS ON)
+
+set(C_dir "${CMAKE_CURRENT_SOURCE_DIR}/C")
+set(CPP_dir "${CMAKE_CURRENT_SOURCE_DIR}/cpp")
+set(tests_dir "${CMAKE_CURRENT_SOURCE_DIR}/test")
+
+add_subdirectory("${C_dir}")
+add_subdirectory("${CPP_dir}")
+
+option(WITH_EXAMPLES "Build examples" OFF)
+if(WITH_EXAMPLES)
+	#file(GLOB EXAMPLES "${tests_dir}/*.c" "${tests_dir}/*.cc" "${tests_dir}/*.cpp")
+	file(GLOB EXAMPLES "${tests_dir}/*.c" "${tests_dir}/*.cpp")
+	foreach(example ${EXAMPLES})
+		detect_dependencies_by_headers("k" "${example}" EXAMPLE_DEPS)
+		get_filename_component(exampleName "${example}" NAME_WE)
+		add_executable("${exampleName}" "${example}")
+		target_link_libraries("${exampleName}" PRIVATE ${PROJECT_NAME} ${EXAMPLE_DEPS})
+	endforeach()
+
+	find_package(ZLIB REQUIRED)
+	target_link_libraries(kseq_test PRIVATE ZLIB::ZLIB)
+	target_link_libraries(kseq_bench PRIVATE ZLIB::ZLIB)
+endif()
+
+option(WITH_DOCS "Build docs" OFF)
+if(WITH_DOCS)
+	find_package(Doxygen REQUIRED dot)
+	load_doxyfile("${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile")
+
+	set(DOXYGEN_PROJECT_BRIEF "${CPACK_PACKAGE_DESCRIPTION}")
+	set(DOXYGEN_USE_MDFILE_AS_MAINPAGE "${CPACK_RESOURCE_FILE_README}")
+
+	set("DOXYGEN_GENERATE_HTML" YES)
+	set("DOXYGEN_GENERATE_MAN" YES)
+
+	if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+		message(STATUS "Compiler is CLang, enabling CLang-assisted parsing in Doxygen.")
+		set(DOXYGEN_CLANG_ASSISTED_PARSING YES)
+		list(JOIN C_SUBLIBS " -I" DOXYGEN_CLANG_OPTIONS)
+		set(DOXYGEN_CLANG_OPTIONS "-I${C_dir} -I${CPP_dir} -I${Include_dir} -I${DOXYGEN_CLANG_OPTIONS}")
+	endif()
+
+	set(DOXYGEN_EXAMPLE_PATH "${tests_dir}")
+	set(DOXYGEN_STRIP_FROM_PATH "${Include_dir}")
+	set(DOXYGEN_STRIP_FROM_INC_PATH "${Include_dir}")
+
+
+	file(GLOB SOURCES_TO_DOCUMENT "${C_dir}/*.[hc]" "${CPP_dir}/*.[ch]xx" "${CPP_dir}/*.[ch]pp")
+	doxygen_add_docs(docs
+		"${SOURCES_TO_DOCUMENT}"
+		ALL
+		USE_STAMP_FILE
+	)
+endif()
+
+#pass_through_cpack_vars()
+
+include(CPack)