Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 25 May 2020 11:58:02 +0200
Description: Use Debian packaged bamtools
 Note: Tiddit source came with a patched BamTools.  The Debian packaged bamtools
       has taken it over in
    https://salsa.debian.org/med-team/bamtools/-/blob/master/debian/patches/tiddit.patch

--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,8 +14,8 @@ set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOU
 set( CMAKE_BUILD_TYPE Release )
 
 include_directories("${PROJECT_SOURCE_DIR}/src")
-include_directories("${PROJECT_SOURCE_DIR}/lib/")
-include_directories("${PROJECT_SOURCE_DIR}/lib/bamtools/src")
+#include_directories("${PROJECT_SOURCE_DIR}/lib/")
+#include_directories("${PROJECT_SOURCE_DIR}/lib/bamtools/src")
 
 
 # source code
@@ -28,10 +28,17 @@ file(GLOB TIDDIT_FILES
 )
 
 
-add_subdirectory(lib)
-
+# add_subdirectory(lib)
+find_path(bamtools_INCLUDE_DIR api/BamReader.h
+                  HINTS ENV BAMTOOLS_INC
+                  PATH_SUFFIXES bamtools
+         )
+set(bamtools_INCLUDE_DIRS ${bamtools_INCLUDE_DIR})
+# the code above does not seem to have the wanted effect
+include_directories(/usr/include/bamtools)
+find_library(BAMTOOLS_LIBRARIES libbamtools.a)
 
 # TIDDIT executable
 add_executable(TIDDIT ${TIDDIT_FILES})
 target_link_libraries(TIDDIT ${ZLIB_LIBRARIES})
-target_link_libraries(TIDDIT  BamTools)
+target_link_libraries(TIDDIT  bamtools)