Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Increase portability by using SIMD Everywhere library
Forwarded: https://github.com/vgteam/gssw/pull/27
Forwarded: https://github.com/ocxtal/dozeu/pull/2
Forwarded: https://github.com/vgteam/libbdsg/pull/72
Forwarded: https://github.com/vgteam/structures/pull/11
Forwarded: https://github.com/vgteam/vg/pull/2867

FIXME: Please check whether changing deps/gssw/src/main.c is really required - I blindly took over our old patch (Andreas Tille)

--- a/deps/gssw/src/main.c
+++ b/deps/gssw/src/main.c
@@ -6,6 +6,8 @@
 
 #include <stdlib.h>
 #include <stdint.h>
+#define SIMDE_ENABLE_NATIVE_ALIASES
+#include "simde/x86/sse2.h"
 #include <zlib.h>
 #include <stdio.h>
 #include <time.h>
--- a/deps/sdsl-lite/CMakeLists.txt
+++ b/deps/sdsl-lite/CMakeLists.txt
@@ -82,19 +82,6 @@ if( MODE_TI )
   endif()
 endif()
 
-include(CheckSSE4_2)
-if( BUILTIN_POPCNT )
-  if( CMAKE_COMPILER_IS_GNUCXX )
-    append_cxx_compiler_flags("-msse4.2 -march=native" "GCC" CMAKE_CXX_OPT_FLAGS)
-  endif()
-  if( CMAKE_COMPILER_IS_GNUCXX )
-    append_cxx_compiler_flags("-msse4.2 -march=native" "CLANG" CMAKE_CXX_OPT_FLAGS)
-  endif()
-  if( CMAKE_COMPILER_IS_INTEL )
-    append_cxx_compiler_flags("-msse4.2 -march=native" "INTEL" CMAKE_CXX_FLAGS)
-  endif()
-endif()
-
 # check for demangle support to get pretty C++ class names
 include(FindCxaDemangle)
 if( HAVE_CXA_DEMANGLE )
--- a/Makefile
+++ b/Makefile
@@ -16,7 +16,8 @@ INC_DIR:=include
 CWD:=$(shell pwd)
 CXX ?= g++
 
-EXE:=vg
+SFX :=
+EXE:=vg$(SFX)
 
 all: $(BIN_DIR)/$(EXE)
 
@@ -624,7 +625,6 @@ clean-vg:
 	$(RM) -f $(INC_DIR)/vg_system_version.hpp
 
 clean:
-	$(RM) -r $(BIN_DIR)
 	$(RM) -r $(LIB_DIR)
 	$(RM) -r $(UNITTEST_OBJ_DIR)
 	$(RM) -r $(SUBCOMMAND_OBJ_DIR)
