Description: patch options for auxprogs Makefiles 
Author: Sascha Steinbiss <sascha@steinbiss.name> 
--- a/auxprogs/bam2hints/Makefile
+++ b/auxprogs/bam2hints/Makefile
@@ -1,5 +1,5 @@
 #	Makefile corresponding to BAM2HINTS
-#	
+#
 # 	NOTE:
 #	a) "-g" option allows for debugging
 #	b) libbamtools.a and lz library are used during the linking process
@@ -17,7 +17,7 @@
 LINK.cc = g++
 
 # Recipe(s)
-# $@: full target name of current target. 
+# $@: full target name of current target.
 # $<: .c file of target. 
 bam2hints : $(OBJECTS) 
 	$(LINK.cc) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS) 
@@ -26,7 +26,7 @@
 all:$(OBJECTS) # Compiles each foo.cc into foo.o
 
 bam2hints.o : $(SOURCES)
-	$(LINK.cc) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -c $< -o $@ -I$(INCLUDES) 
+	$(LINK.cc) $(CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) -c $< -o $@ -I$(INCLUDES)
 
 clean:
 	rm -f bam2hints.o bam2hints ../../bin/bam2hints
