Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Enable the passing of extra compilation flags, for hardening
--- a/Makefile
+++ b/Makefile
@@ -157,7 +157,7 @@ SSE_FLAG=-msse2
 
 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
@@ -255,7 +255,7 @@ hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS
 	$(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) \
@@ -264,7 +264,7 @@ hisat-bp-bin-debug: hisat_bp.cpp $(SEARC
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT_CPPS_MAIN) \
-	$(LIBS) $(SEARCH_LIBS)
+	$(LIBS) $(SEARCH_LIBS) $(LDFLAGS)
 
 
 #
@@ -277,7 +277,7 @@ hisat2-build-s: hisat2_build.cpp $(SHARE
 	$(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) \
@@ -285,7 +285,7 @@ hisat2-build-l: hisat2_build.cpp $(SHARE
 	$(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) \
@@ -293,7 +293,7 @@ hisat2-build-s-debug: hisat2_build.cpp $
 	$(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) \
@@ -301,7 +301,7 @@ hisat2-build-l-debug: hisat2_build.cpp $
 	$(INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \
-	$(LIBS) $(BUILD_LIBS)
+	$(LIBS) $(BUILD_LIBS) $(LDFLAGS)
 
 #
 # hisat2 targets
@@ -313,7 +313,7 @@ hisat2-align-s: hisat2.cpp $(SEARCH_CPPS
 	$(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) \
@@ -321,7 +321,7 @@ hisat2-align-l: hisat2.cpp $(SEARCH_CPPS
 	$(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) \
@@ -330,7 +330,7 @@ hisat2-align-s-debug: hisat2.cpp $(SEARC
 	$(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) \
@@ -339,7 +339,7 @@ hisat2-align-l-debug: hisat2.cpp $(SEARC
 	$(INC) $(SEARCH_INC) \
 	-o $@ $< \
 	$(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \
-	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS)
+	$(LIBS) $(SRA_LIB) $(SEARCH_LIBS) $(LDFLAGS)
 
 #
 # hisat2-inspect targets
@@ -352,7 +352,7 @@ hisat2-inspect-s: hisat2_inspect.cpp $(H
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS)
 	$(CXX) $(RELEASE_FLAGS) \
@@ -361,7 +361,7 @@ hisat2-inspect-l: hisat2_inspect.cpp $(H
 	$(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) \
@@ -370,7 +370,7 @@ hisat2-inspect-s-debug: hisat2_inspect.c
 	$(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) \
@@ -379,7 +379,7 @@ hisat2-inspect-l-debug: hisat2_inspect.c
 	$(INC) -I . \
 	-o $@ $< \
 	$(SHARED_CPPS) \
-	$(LIBS) $(INSPECT_LIBS)
+	$(LIBS) $(INSPECT_LIBS) $(LDFLAGS)
 
 
 
