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use the simde header library for greater compatibility #251

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9586a59
use the simde header library for greater compatibility
mr-c Jun 20, 2020
4d80442
compilation fixes
mr-c Feb 15, 2023
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3 changes: 3 additions & 0 deletions .gitmodules
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
[submodule "simde"]
path = simde
url = https://github.com/nemequ/simde-no-tests
20 changes: 11 additions & 9 deletions Makefile
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Expand Up @@ -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 =
Expand Down Expand Up @@ -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,$(ARCH))
BITS=64
endif
# msys will always be 32 bit so look at the cpu arch instead.
Expand All @@ -165,14 +166,15 @@ ifneq (,$(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)\""
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3 changes: 2 additions & 1 deletion aligner_sw.h
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Expand Up @@ -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"
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2 changes: 1 addition & 1 deletion alphabet.cpp
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Expand Up @@ -400,7 +400,7 @@ int dnacomp[5] = {

const char *iupacs = "!ACMGRSVTWYHKDBN!acmgrsvtwyhkdbn";

char mask2iupac[16] = {
int mask2iupac[16] = {
-1,
'A', // 0001
'C', // 0010
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2 changes: 1 addition & 1 deletion alphabet.h
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Expand Up @@ -65,7 +65,7 @@ extern uint8_t dinuc2color[5][5];
/// corresponding 2-bit nucleotide
extern uint8_t nuccol2nuc[5][5];
/// Convert a 4-bit mask into an IUPAC code
extern char mask2iupac[16];
extern int mask2iupac[16];

/// Convert an ascii color to an ascii dna char
extern char col2dna[];
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5 changes: 2 additions & 3 deletions processor_support.h
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Expand Up @@ -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)
Expand Down Expand Up @@ -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;
}
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1 change: 1 addition & 0 deletions simde
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Submodule simde added at 3698ce
4 changes: 3 additions & 1 deletion sse_util.h
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Expand Up @@ -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:
Expand Down
2 changes: 1 addition & 1 deletion sstring.h
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Expand Up @@ -3326,7 +3326,7 @@ class SDnaMaskString : public SStringExpandable<char, S, M> {
*/
char toChar(size_t idx) const {
assert_range((int)this->cs_[idx], 0, 15);
return mask2iupac[(int)this->cs_[idx]];
return (char)mask2iupac[(int)this->cs_[idx]];
}

/**
Expand Down