Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Enable the passing of extra compilation flags, for hardening
--- hisat2.orig/Makefile
+++ hisat2/Makefile
@@ -157,7 +157,7 @@
 
 DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
+RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 $(CPPFLAGS)
 RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
 NOASSERT_FLAGS = -DNDEBUG
 FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
@@ -253,7 +253,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
-	$(LIBS) $(SEARCH_LIBS)
+	$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
 
 hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 	$(CXX) $(DEBUG_FLAGS) \
@@ -262,7 +262,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
-	$(LIBS) $(SEARCH_LIBS)
+	$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
 
 
 #
@@ -275,7 +275,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
+	$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
 
 hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
@@ -283,7 +283,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
+	$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
 
 hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
 	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
@@ -291,7 +291,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
+	$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
 
 hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS)
 	$(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
@@ -299,7 +299,7 @@
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
+	$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
 
 #
 # hisat2 targets
@@ -311,7 +311,7 @@
 	$(INC) $(SEARCH_INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
+	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS) $(LDFLAGS)
 
 hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 	$(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \
@@ -319,7 +319,7 @@
 	$(INC) $(SEARCH_INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
+	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS) $(LDFLAGS)
 
 hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 	$(CXX) $(DEBUG_FLAGS) \
@@ -328,7 +328,7 @@
 	$(INC) $(SEARCH_INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
+	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS) $(LDFLAGS)
 
 hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS)
 	$(CXX) $(DEBUG_FLAGS) \
@@ -337,7 +337,7 @@
 	$(INC) $(SEARCH_INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
+	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS) $(LDFLAGS)
 
 #
 # hisat2-inspect targets
@@ -350,7 +350,7 @@
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
 	$(CXX) $(RELEASE_FLAGS) \
@@ -359,7 +359,7 @@
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
 	$(CXX) $(DEBUG_FLAGS) \
@@ -368,7 +368,7 @@
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) 
 	$(CXX) $(DEBUG_FLAGS) \
@@ -377,7 +377,7 @@
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 
 
