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Description: use more Debian packaged libraries
Author: Sascha Steinbiss <satta@debian.org>,
Michael R. Crusoe <michael.crusoe@gmail.com>
--- a/assembler/src/cmake/includes.cmake
+++ b/assembler/src/cmake/includes.cmake
@@ -3,6 +3,8 @@
set(CMAKE_INCLUDE_CURRENT_DIR ON)
set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
+include_directories("/usr/include")
+include_directories(SYSTEM "/usr/include")
include_directories(${SPADES_MAIN_INCLUDE_DIR} ${SPADES_BUILT_INCLUDE_DIR} ${CMAKE_SOURCE_DIR} ${SPADES_MODULES_DIR})
include_directories(SYSTEM "${EXT_DIR}/include")
include_directories(SYSTEM "${ZLIB_INCLUDE_DIRS}")
--- a/assembler/src/common/assembly_graph/CMakeLists.txt
+++ b/assembler/src/common/assembly_graph/CMakeLists.txt
@@ -9,4 +9,4 @@ project(assembly_graph CXX)
add_library(assembly_graph STATIC
components/connected_component.cpp paths/bidirectional_path.cpp paths/bidirectional_path_io/io_support.cpp paths/bidirectional_path_io/bidirectional_path_output.cpp graph_support/scaff_supplementary.cpp ../modules/alignment/edge_index_refiller.cpp graph_support/coverage_uniformity_analyzer.cpp)
-target_link_libraries(assembly_graph hattrie)
+target_link_libraries(assembly_graph hat-trie)
--- a/assembler/src/common/modules/alignment/kmer_map.hpp
+++ b/assembler/src/common/modules/alignment/kmer_map.hpp
@@ -9,7 +9,7 @@
#include "sequence/rtseq.hpp"
-#include <htrie/hat-trie.h>
+#include <hat-trie/hat-trie.h>
#include <boost/iterator/iterator_facade.hpp>
namespace debruijn_graph {
--- a/assembler/src/common/modules/path_extend/overlap_analysis.hpp
+++ b/assembler/src/common/modules/path_extend/overlap_analysis.hpp
@@ -2,7 +2,7 @@
#include "utils/logger/logger.hpp"
#include "sequence/range.hpp"
-#include "ssw/ssw_cpp.h"
+#include "ssw_cpp.h"
namespace debruijn_graph {
--- a/assembler/ext/src/CMakeLists.txt
+++ b/assembler/ext/src/CMakeLists.txt
@@ -1,16 +1,13 @@
# -*- cmake -*-
add_subdirectory(jemalloc)
-add_subdirectory(nlopt)
add_subdirectory(ConsensusCore)
add_subdirectory(bamtools)
add_subdirectory(samtools)
add_subdirectory(cppformat)
-add_subdirectory(ssw)
add_subdirectory(cityhash)
add_subdirectory(getopt_pp)
add_subdirectory(llvm)
-add_subdirectory(htrie)
add_subdirectory(gqf)
add_subdirectory(edlib)
add_subdirectory(gfa1)
--- a/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp
+++ b/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp
@@ -18,7 +18,7 @@
#include <boost/math/distributions/geometric.hpp>
#include <boost/math/distributions/pareto.hpp>
-#include <nlopt/nlopt.hpp>
+#include <nlopt.hpp>
#include <vector>
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