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diff -ur bowtie-1.2.3.org/Makefile bowtie-1.2.3/Makefile
--- bowtie-1.2.3.org/Makefile 2019-09-26 12:14:35.498557693 +0900
+++ bowtie-1.2.3/Makefile 2019-09-26 12:15:17.262960932 +0900
@@ -174,14 +174,22 @@
ifeq (x86_64, $(shell uname -p))
BITS=64
endif
+ ifeq (aarch64, $(shell uname -p))
+ BITS=64
+ endif
endif
ifeq (32,$(BITS))
$(error bowtie2 compilation requires a 64-bit platform )
endif
-DEBUG_FLAGS = -O0 -g3 -m64
-RELEASE_FLAGS = -O3 -m64
+ifeq (aarch64, $(shell uname -p))
+ DEBUG_FLAGS = -O0 -g3
+ RELEASE_FLAGS = -O3
+else
+ DEBUG_FLAGS = -O0 -g3 -m64
+ RELEASE_FLAGS = -O3 -m64
+endif
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
diff -ur bowtie-1.2.3.org/ebwt.h bowtie-1.2.3/ebwt.h
--- bowtie-1.2.3.org/ebwt.h 2019-09-26 12:14:35.518559804 +0900
+++ bowtie-1.2.3/ebwt.h 2019-09-26 14:13:12.142637470 +0900
@@ -1957,7 +1957,11 @@
struct USE_POPCNT_INSTRUCTION {
inline static int pop64(uint64_t x) {
int64_t count;
+#ifdef __aarch64__
+ count = __builtin_popcount(x);
+#else
asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
+#endif
return count;
}
};
diff -ur bowtie-1.2.3.org/third_party/cpuid.h bowtie-1.2.3/third_party/cpuid.h
--- bowtie-1.2.3.org/third_party/cpuid.h 2019-09-26 12:14:35.548562971 +0900
+++ bowtie-1.2.3/third_party/cpuid.h 2019-09-26 12:17:41.677842567 +0900
@@ -65,6 +65,7 @@
#define bit_FSGSBASE (1 << 0)
#define bit_BMI (1 << 3)
+#ifndef __aarch64__
#if defined(__i386__) && defined(__PIC__)
/* %ebx may be the PIC register. */
#if __GNUC__ >= 3
@@ -185,3 +186,13 @@
__cpuid (__level, *__eax, *__ebx, *__ecx, *__edx);
return 1;
}
+#endif
+#ifdef __aarch64__
+static __inline int
+__get_cpuid (unsigned int __level,
+ unsigned int *__eax, unsigned int *__ebx,
+ unsigned int *__ecx, unsigned int *__edx)
+{
+ return 1;
+}
+#endif
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