Description: Add compiler flags necessary for hardening.
Author: Sascha Steinbiss <sascha@steinbiss.name>
--- a/Makefile
+++ b/Makefile
@@ -11,22 +11,22 @@
 
 
 findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
 
 reassemble: src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
 
 variety: src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
 
 mapcontigs: src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
 
 ungap: src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
-	$(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
 
 .cpp.o:
-	$(CXX) $(CXXFLAGS) -c $< -o $@
+	$(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
 
 clean:
 	rm -f *.o
