lh3 · sethbrin · Feb 21, 2017
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,79 @@
+cmake_minimum_required(VERSION 2.8)
+project(bwa)
+
+set(CFLAGS
+    -g
+    -Wall
+    -Wno-unused-function
+    -O2)
+
+set(WRAP_MALLOC
+    -DUSE_MALLOC_WRAPPERS)
+
+set(LIBS
+    m
+    z
+    pthread)
+
+exec_program(uname
+    ARGS -s
+    OUTPUT_VARIABLE target)
+
+if(target STREQUAL "Linux")
+    set(LIBS
+        rt
+        ${LIBS})
+endif()
+
+add_definitions(-DHAVE_PTHREAD ${WRAP_MALLOC})
+string(REPLACE ";" " " CMAKE_C_FLAGS "${CFLAGS}")
+
+set(LOBJS_FILES
+    utils.c
+    kthread.c
+    kstring.c
+    ksw.c
+    bwt.c
+    bntseq.c
+    bwa.c
+    bwamem.c
+    bwamem_pair.c
+    bwamem_extra.c
+    malloc_wrap.c
+    QSufSort.c
+    bwt_gen.c
+    rope.c
+    rle.c
+    is.c
+    bwtindex.c)
+
+set(AOBJS_FILES
+    bwashm.c
+    bwase.c
+    bwaseqio.c
+    bwtgap.c
+    bwtaln.c
+    bamlite.c
+    bwape.c
+    kopen.c
+    pemerge.c
+    maxk.c
+    bwtsw2_core.c
+    bwtsw2_main.c
+    bwtsw2_aux.c
+    bwt_lite.c
+    bwtsw2_chain.c
+    fastmap.c
+    bwtsw2_pair.c)
+
+
+add_library(bwa_static ${LOBJS_FILES})
+
+add_executable(bwa ${AOBJS_FILES} main.c)
+target_link_libraries(bwa bwa_static) 
+
+add_executable(bwamem-lite example.c)
+target_link_libraries(bwamem-lite bwa_static) 
+
+target_link_libraries(bwa ${LIBS})
+target_link_libraries(bwamem-lite ${LIBS})