Critical: ProphEx cannot be compiled on M1 (new macs)

[karel-brinda]

/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"

s -g -O2  prophyle_assembler.o -o prophyle_assembler -L. -lz
/Library/Developer/CommandLineTools/usr/bin/make -C prophyle_index
/Library/Developer/CommandLineTools/usr/bin/make -C bwa
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
In file included from ksw.c:29:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
In file included from ksw.c:29:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
In file included from ksw.c:29:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/emmintrin.h:17:
In file included from /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/xmmintrin.h:17:
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
#error "This header is only meant to be used on x86 and x64 architecture"
 ^
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:54:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:133:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packsswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:163:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packssdw((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/mmintrin.h:193:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size

[martin-g]

Since 0.7.18 (lh3/bwa@79b230d) BWA support ARM64 architecture!
I guess you will need to update the local copy of bwa - https://github.com/prophyle/prophex/tree/master/src/bwa.

[karel-brinda]

Thanks for the pointer!

[karel-brinda]

Note to myself: BWA is not a submodule as there were some changes (probably reported timing or st like that).

Steps:

• identify the original version of bwa used
• make a diff
• update bwa
• backpropagate the diff