Fix sts without beagle

Author: 4ment

CMakeLists.txt

@@ -72,6 +72,7 @@ IF(USE_BEAGLE)
 	link_directories(${HMS_BEAGLE_LIBRARY_DIRS})
 ELSE(USE_BEAGLE)
 	SET(NO_BEAGLE "1")
+	add_definitions("-DNO_BEAGLE")
 ENDIF(USE_BEAGLE)
 
 # Bio++

src/CMakeLists.txt

@@ -6,6 +6,11 @@ configure_file (
 include_directories("${CMAKE_CURRENT_SOURCE_DIR}/online")
 file(GLOB STS_CPP_FILES ${CMAKE_CURRENT_SOURCE_DIR}/online/*.cc)
 
+IF(NO_BEAGLE)
+	list(REMOVE_ITEM STS_CPP_FILES "${CMAKE_CURRENT_SOURCE_DIR}/online/beagle_flexible_tree_likelihood.cc")
+	list(REMOVE_ITEM STS_CPP_FILES "${CMAKE_CURRENT_SOURCE_DIR}/online/beagle_tree_likelihood.cc")
+ENDIF(NO_BEAGLE)
+
 add_library(sts-static STATIC ${STS_CPP_FILES})
 
 set(STS_PHYLO_LIBS

src/online/util.cc

@@ -3,7 +3,9 @@
 ///
 #include "util.h"
 
+#ifndef NO_BEAGLE
 #include "libhmsbeagle/beagle.h"
+#endif
 
 #include <Bpp/Phyl/PatternTools.h>
 #include <Bpp/Seq/Container/SequenceContainer.h>
@@ -87,7 +89,7 @@ bpp::SiteContainer* unique_sites(const bpp::SiteContainer& sites, bool verbose)
     return compressed;
 }
 
-
+#ifndef NO_BEAGLE
 std::string beagle_errstring(const int beagle_error_code)
 {
     switch(beagle_error_code) {
@@ -109,7 +111,7 @@ void beagle_check(int return_code)
     if(return_code != BEAGLE_SUCCESS)
         throw std::runtime_error(sts::util::beagle_errstring(return_code));
 }
-
+#endif
 
 double effectiveSampleSize(const std::vector<double>& logWeights)
 {

test/test_sts_flexible_tree_likelihood.cpp

@@ -376,6 +376,8 @@ void testAttachmentLikelihoodDeriv(const std::string& tree_path, const std::stri
     ASSERT_FALSE(tree->isMultifurcating());
 
 	std::vector<string> names = aln->getSequencesNames();
+	tree->getRootNode()->getSon(0)->setDistanceToFather(tree->getRootNode()->getSon(0)->getDistanceToFather()+tree->getRootNode()->getSon(1)->getDistanceToFather());
+	tree->getRootNode()->getSon(1)->setDistanceToFather(1e-6);
 
     for(const string& leafName : tree->getLeavesNames()) {
         bpp::TreeTemplate<Node> tmpTree(*tree);