Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil

algo/Makefile

 CC=g++
-OPTIM=-O2 
+OPTIM=-O2 -DNDEBUG
 CXXFLAGS=-W -Wall $(OPTIM) $(DEBUG) $(CONFIG)
 LDFLAGS=-lm
 EXEC=vidjil kmer kmer_count cut count detailed_affect
@@ -43,7 +43,7 @@ debug:
 	make DEBUG="-ggdb"
 
 $(EXEC): %: %.o 
-	make -C core
+	make -C core OPTIM="$(OPTIM)"
 	$(CC) -o $(BINDIR)/$@ $^ $(LIBCORE) $(LDFLAGS) $(CXXFLAGS)
 
 clean:
@@ -53,6 +53,7 @@ clean:
 
 forcedep:
 	g++ -M $(MAINCORE) > dep.mk
+	make -C core forcedep
 
 DEP=$(wildcard dep.mk)
 

algo/core/Makefile

@@ -5,6 +5,8 @@ SRCCORE=$(wildcard *.cpp)
 OBJCORE=$(SRCCORE:.cpp=.o)
 LIBCORE=vidjil.a
 
+.PHONY: all clean forcedep
+
 all: $(LIBCORE)
 
 $(LIBCORE): $(OBJCORE)
@@ -13,6 +15,9 @@ $(LIBCORE): $(OBJCORE)
 clean:
 	rm -f $(OBJCORE) $(LIBCORE)
 
+forcedep:
+	g++ -M $(SRCCORE) > dep.mk
+
 DEP=$(wildcard dep.mk)
 
 ifeq (${DEP},)

algo/vidjil.cpp

@@ -952,9 +952,6 @@ int main (int argc, char **argv)
 	  {
 	    
 	    // As soon as one representative is segmented
-	    
-	    representatives.push_back(seg.getSequence());
-            representatives_labels.push_back("#" + string_of_int(num_clone));
 
               // We need to find the window in the representative
               size_t window_pos = seg.getSequence().sequence.find(it->first);
@@ -1040,6 +1037,10 @@ int main (int argc, char **argv)
 
         if (seg.isSegmented() 
             || it == --(sort_windows.end())) {
+	  // Store the representative and its label
+          representatives.push_back(representative);
+          representatives_labels.push_back("#" + string_of_int(num_clone));
+
               // display window
               cout << endl 
 		   << ">clone-"  << setfill('0') << setw(WIDTH_NB_CLONES) << num_clone << "-window"  << " " << windows_labels[it->first] << endl