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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)
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