Init cmake

CMakeLists.txt

@@ -0,0 +1,21 @@
+cmake_minimum_required(VERSION 3.10)
+
+# Project name and version
+project(ivar VERSION 2.0)
+
+# Enable testing
+enable_testing()
+
+# Specify the C++ standard
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -O2")
+
+# Add subdirectories
+add_subdirectory(src)
+add_subdirectory(tests)
+
+
+# Installation rules
+install(TARGETS ivar DESTINATION bin)

src/CMakeLists.txt

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+# Add library or executable target
+file(GLOB armadillo_src
+        "include/armadillo_bits/*.hpp"
+)
+
+add_executable(ivar
+        ivar.cpp
+        call_consensus_pileup.cpp
+        alignment.cpp
+        suffix_tree.cpp
+        trim_primer_quality.cpp
+        remove_reads_from_amplicon.cpp
+        call_variants.cpp
+        primer_bed.cpp
+        allele_functions.cpp
+        get_masked_amplicons.cpp
+        get_common_variants.cpp
+        parse_gff.cpp
+        ref_seq.cpp
+        interval_tree.cpp
+        saga.cpp
+        gmm.cpp
+        population_estimate.cpp
+        call_consensus_clustering.cpp
+        ${armadillo_src}
+)
+
+target_link_libraries(ivar z pthread)
+
+if(HTSLIB_PREFIX)
+    find_library(HTSLIB
+            NAMES hts
+            PATHS ${HTSLIB_PREFIX}/lib
+            NO_DEFAULT_PATH)
+else()
+    find_library(HTSLIB
+            NAMES hts)
+endif()
+
+if(NOT HTSLIB)
+    message(FATAL_ERROR "htslib not found")
+else()
+    target_link_libraries(ivar ${HTSLIB})
+endif()
+
+if(HTSLIB_PREFIX)
+    target_include_directories(ivar PRIVATE ${HTSLIB_PREFIX}/include)
+else()
+    message(FATAL_ERROR "htslib header files not found")
+endif()
+
+# Specify include directories if needed
+#target_include_directories(ivar PUBLIC ${PROJECT_SOURCE_DIR}/include)