Description: Inject architecture specific flags:
 - For amd64 and i386 add -mtune=generic and -msse3,
 - use -fsigned-char for all architectures and place it in the very beginning
   of CFLAGS, otherwise test fail on architecrures with unsigned char 
   signedness
 - Change -O9 to -O3 because -O levels higher than 3 have no effect
 - Append CFLAGS and LDFLAGS instead of hardcoding the values, this way the 
   hardening flags are set correctly
Author: Alex Mestiashvili <alex@biotec.tu-dresden.de>
--- a/src/Makefile.Linux
+++ b/src/Makefile.Linux
@@ -2,10 +2,10 @@
 
 include makefile.version
 
-OPT_LEVEL = 9
-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
-LDFLAGS = ${STATIC_MAKE} -lpthread -lz -lm ${MACOS} -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
-CC = gcc ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 
+OPT_LEVEL = 3
+CCFLAGS += -O${OPT_LEVEL} -fsigned-char -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\"  -D_FILE_OFFSET_BITS=64
+LDFLAGS += ${STATIC_MAKE} -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
+CC = gcc ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -ggdb -fomit-frame-pointer -ffast-math -funroll-loops -fmessage-length=0
 
 
 ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib