[med-svn] [Git][med-team/berkeley-express][upstream] New upstream version 1.5.3+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / berkeley-express


Commits:
b0d54647 by Michael R. Crusoe at 2019-11-17T15:24:35Z
New upstream version 1.5.3+dfsg
- - - - -


3 changed files:

- CMakeLists.txt
- src/CMakeLists.txt
- src/targets.cpp


Changes:

=====================================
CMakeLists.txt
=====================================
@@ -6,6 +6,9 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)
 set(${PROJECT_NAME}_VERSION_MINOR 5)
 set(${PROJECT_NAME}_VERSION_PATCH 1)
 
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 set(CMAKE_CXX_FLAGS "-Wall")
 
 set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}")


=====================================
src/CMakeLists.txt
=====================================
@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)
 
 add_executable(express ${sources} ${headers} ${PROTO_SOURCES} ${PROTO_HEADERS})
 
-set(LIBRARIES ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} ${BAMTOOLS_LIBRARIES})
+set(LIBRARIES ${Boost_LIBRARIES} ${BAMTOOLS_LIBRARIES} ${ZLIB_LIBRARIES})
 
 if (GPERFTOOLS_TCMALLOC) 
    set(LIBRARIES ${LIBRARIES} "libtcmalloc_minimal.a")
@@ -20,7 +20,9 @@ endif(PROTOBUF_FOUND)
 
 if (WIN32)
 target_link_libraries(express ${LIBRARIES})
-else(WIN32)
+elseif(APPLE)
+target_link_libraries(express ${LIBRARIES} pthread)
+elseif(UNIX)
 target_link_libraries(express ${LIBRARIES} pthread rt)
-endif(WIN32)
+endif()
 install(TARGETS express DESTINATION bin)


=====================================
src/targets.cpp
=====================================
@@ -113,12 +113,12 @@ double Target::sample_likelihood(bool with_pseudo,
 
   double ll = LOG_1;
   double tot_mass = mass(with_pseudo);
-  double tot_eff_len = cached_effective_length(lib.bias_table);
+  double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table));
   if (neighbors) {
     foreach (const Target* neighbor, *neighbors) {
       tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo));
       tot_eff_len = log_add(tot_eff_len,
-                            neighbor->cached_effective_length(lib.bias_table));
+                            neighbor->cached_effective_length(static_cast<bool>(lib.bias_table)));
     }
   }
   ll += tot_mass - tot_eff_len;



View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002

-- 
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002
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