Package: spades / 3.13.1+dfsg-2

0114_use_debian_provided_libs.patch Patch series | download
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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>