use the simde header library for greater compatibility

Author: mr-c

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "simde"]
+	path = simde
+	url = https://github.com/nemequ/simde-no-tests

Makefile

@@ -55,7 +55,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
 	MACOS = 1
 endif
 
-EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11
+EXTRA_FLAGS += -std=c++11
 INC += -I. -I third_party 
 
 MM_DEF = 
@@ -152,9 +152,10 @@ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
 SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
 VERSION = $(shell cat VERSION)
 
+ARCH=$(shell uname -m)
 # Convert BITS=?? to a -m flag
 BITS=32
-ifeq (x86_64,$(shell uname -m))
+ifeq (x86_64,$(ARCH))
 BITS=64
 endif
 # msys will always be 32 bit so look at the cpu arch instead.
@@ -165,14 +166,15 @@ ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
 endif
 BITS_FLAG =
 
-ifeq (32,$(BITS))
-	BITS_FLAG = -m32
-endif
-
-ifeq (64,$(BITS))
-	BITS_FLAG = -m64
+ifeq (x86_64,$(ARCH))
+	ifeq (32,$(BITS))
+		BITS_FLAG = -m32
+	endif
+	ifeq (64,$(BITS))
+		BITS_FLAG = -m64
+	endif
+	SSE_FLAG=-msse2
 endif
-SSE_FLAG=-msse2
 
 DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
 DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""

aligner_sw.h

@@ -66,11 +66,12 @@
 
 #define INLINE_CUPS
 
+#define SIMDE_ENABLE_NATIVE_ALIASES
+#include <simde/x86/sse2.h>
 #include <stdint.h>
 #include <iostream>
 #include <limits>
 #include "threading.h"
-#include <emmintrin.h>
 #include "aligner_sw_common.h"
 #include "aligner_sw_nuc.h"
 #include "ds.h"

processor_support.h

@@ -12,7 +12,7 @@
 
 #if defined(__INTEL_COMPILER)
 #   define USING_INTEL_COMPILER
-#elif defined(__GNUC__)
+#elif defined(__GNUC__) && defined(__x86_64__) || defined(__i386__)
 #   define USING_GCC_COMPILER
 #   include <cpuid.h>
 #elif defined(_MSC_VER)
@@ -52,8 +52,7 @@ class ProcessorSupport {
 #elif defined(USING_GCC_COMPILER)
         __get_cpuid(0x1, &regs.EAX, &regs.EBX, &regs.ECX, &regs.EDX);
 #else
-        std::cerr << "ERROR: please define __cpuid() for this build.\n"; 
-        assert(0);
+	return false;
 #endif
         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
     }

simde

@@ -20,11 +20,13 @@
 #ifndef SSE_UTIL_H_
 #define SSE_UTIL_H_
 
+#define SIMDE_ENABLE_NATIVE_ALIASES
+#include <simde/x86/sse2.h>
+
 #include "assert_helpers.h"
 #include "ds.h"
 #include "limit.h"
 #include <iostream>
-#include <emmintrin.h>
 
 class EList_m128i {
 public: