The libdna from kloetzl

dnax_count_mismatches_wg

Count substitutions with gaps. How should the interface look like?

dna4_revcomp

Solve these issues before release.

Finish the implementation.
Write documentation. Cancelled in favor of manpage.
Write a manpage. a49ee16
Create unit tests. Verify the all implementations. 1f3d84e
Verify dispatching. 2dca9e7
Check exported symbols.

dnax_translate

Improve the implementation. At the moment it is basically a glorified switch-statement. What would be a better design?

release v1.4

Add an option to build without ifunc for CI.
fix #17

release v1.2

Planned features:

#8
rename dna4_count_mismatches_rev to dna4_count_mismatches_rc.
#16
create example for printing random fasta file
create example for computing visual fingerprint using minimizers.
make tests and benchmarks use fill_random

Fix .symbol_resolver on macOS

Recently, the symbol_resolver mechanism broke. Not sure that was caused by a macOS update or LLVM or something else. Now macOS has to fallback to the manual resolver.

Add a unit test for the manual resolver.
Figure out why the .symbol resolver method no longer works. See code example here, here or here.

Naming inconsistency

We have dna4_count_mismatches, but dnax_find_first_mismatch. There is no technical reason why the former is restricted to DNA4. It should be renamed to dnax_count_mismatches.

ARM performance optimisations

At the moment, all hand written optimisations are for x86. However, ARM is on the rise. Can the current strategies be ported to ARM using simde or is manual optimisation better?

release v1.1

This issue is used to track the progress on release v1.1. I am planning to implement the following features:

optimizations on arm #10
improve dna4_revcomp on x86 #11
dnax_extract_dna4 (done for x86)

Counting substitutions is already implemented in dna4_count_mismatches. However, DNA has two strands. When the two strings come from different strains, a new function can be useful. An example implementation is build in phylonium.

Python wrapper

Provide a Python API to access the C functions. Things to consider:

Which functions, all functions?
Best interface?
Compatibility to BioPython

release v1.3

Planned features:

Doesn't compile on non-x86 targets

It appears that the SSE4.2 and AVX implementations are compiled unconditionally, even on non-x86 platforms. This leads to build failure (here on arm64 FreeBSD 12.2):

$ uname -mrs                                                                     
FreeBSD 12.2-RELEASE arm64

$ meson compile
Found runner: ['/usr/local/bin/ninja']
ninja: Entering directory `.'
[1/24] Compiling C object libdna.so.0.p/src_dna4_count_mismatches.c.o
FAILED: libdna.so.0.p/src_dna4_count_mismatches.c.o 
cc -Ilibdna.so.0.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O2 -fvisibility=hidden -MD -MQ libdna.so.0.p/src_dna4_count_mismatches.c.o -MF libdna.so.0.p/src_dna4_count_mismatches.c.o.d -o libdna.so.0.p/src_dna4_count_mismatches.c.o -c ../src/dna4_count_mismatches.c
../src/dna4_count_mismatches.c:42:2: error: use of unknown builtin '__builtin_cpu_init' [-Wimplicit-function-declaration]
        __builtin_cpu_init();
        ^
../src/dna4_count_mismatches.c:44:6: error: use of unknown builtin '__builtin_cpu_supports' [-Wimplicit-function-declaration]
        if (__builtin_cpu_supports("avx512bw") &&
            ^
../src/dna4_count_mismatches.c:44:6: note: did you mean '__builtin_cpu_init'?
../src/dna4_count_mismatches.c:42:2: note: '__builtin_cpu_init' declared here
        __builtin_cpu_init();
        ^
2 errors generated.
[2/24] Compiling C object libsse42lib.a.p/src_dna4_count_mismatches_sse42.c.o
FAILED: libsse42lib.a.p/src_dna4_count_mismatches_sse42.c.o 
cc -Ilibsse42lib.a.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O3 -mpopcnt -msse4.2 -fvisibility=hidden -MD -MQ libsse42lib.a.p/src_dna4_count_mismatches_sse42.c.o -MF libsse42lib.a.p/src_dna4_count_mismatches_sse42.c.o.d -o libsse42lib.a.p/src_dna4_count_mismatches_sse42.c.o -c ../src/dna4_count_mismatches_sse42.c
cc: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-msse4.2' [-Wunused-command-line-argument]
In file included from ../src/dna4_count_mismatches_sse42.c:10:
In file included from /usr/lib/clang/10.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/10.0.1/include/xmmintrin.h:13:
/usr/lib/clang/10.0.1/include/mmintrin.h:50:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:129:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:159:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:189:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:216:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:239:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:260:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:287:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:310:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:331:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:352:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:373:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:394:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:416:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:439:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:461:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:483:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:504:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:525:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[3/24] Compiling C object libsse42lib.a.p/src_dna4_revcomp_sse42.c.o
FAILED: libsse42lib.a.p/src_dna4_revcomp_sse42.c.o 
cc -Ilibsse42lib.a.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O3 -mpopcnt -msse4.2 -fvisibility=hidden -MD -MQ libsse42lib.a.p/src_dna4_revcomp_sse42.c.o -MF libsse42lib.a.p/src_dna4_revcomp_sse42.c.o.d -o libsse42lib.a.p/src_dna4_revcomp_sse42.c.o -c ../src/dna4_revcomp_sse42.c
cc: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-msse4.2' [-Wunused-command-line-argument]
In file included from ../src/dna4_revcomp_sse42.c:10:
In file included from /usr/lib/clang/10.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/10.0.1/include/xmmintrin.h:13:
/usr/lib/clang/10.0.1/include/mmintrin.h:50:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:129:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:159:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:189:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:216:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:239:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:260:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:287:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:310:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:331:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:352:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:373:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:394:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:416:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:439:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:461:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:483:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:504:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:525:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[4/24] Compiling C object libavx512lib.a.p/src_dna4_count_mismatches_avx512.c.o
FAILED: libavx512lib.a.p/src_dna4_count_mismatches_avx512.c.o 
cc -Ilibavx512lib.a.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O3 -mpopcnt -mavx512bw -mavx512vl -fvisibility=hidden -MD -MQ libavx512lib.a.p/src_dna4_count_mismatches_avx512.c.o -MF libavx512lib.a.p/src_dna4_count_mismatches_avx512.c.o.d -o libavx512lib.a.p/src_dna4_count_mismatches_avx512.c.o -c ../src/dna4_count_mismatches_avx512.c
cc: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-mavx512bw' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-mavx512vl' [-Wunused-command-line-argument]
In file included from ../src/dna4_count_mismatches_avx512.c:10:
In file included from /usr/lib/clang/10.0.1/include/immintrin.h:14:
/usr/lib/clang/10.0.1/include/mmintrin.h:50:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:129:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:159:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:189:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:216:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:239:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:260:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:287:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:310:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:331:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:352:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:373:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:394:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:416:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:439:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:461:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:483:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:504:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:525:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[5/24] Compiling C object libavx2lib.a.p/src_dna4_count_mismatches_avx2.c.o
FAILED: libavx2lib.a.p/src_dna4_count_mismatches_avx2.c.o 
cc -Ilibavx2lib.a.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O3 -mpopcnt -mavx2 -fvisibility=hidden -MD -MQ libavx2lib.a.p/src_dna4_count_mismatches_avx2.c.o -MF libavx2lib.a.p/src_dna4_count_mismatches_avx2.c.o.d -o libavx2lib.a.p/src_dna4_count_mismatches_avx2.c.o -c ../src/dna4_count_mismatches_avx2.c
cc: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-mavx2' [-Wunused-command-line-argument]
In file included from ../src/dna4_count_mismatches_avx2.c:10:
In file included from /usr/lib/clang/10.0.1/include/immintrin.h:14:
/usr/lib/clang/10.0.1/include/mmintrin.h:50:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:129:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:159:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:189:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:216:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:239:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:260:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:287:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:310:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:331:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:352:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:373:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:394:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:416:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:439:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:461:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:483:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:504:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:525:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
[6/24] Compiling C object libavx2lib.a.p/src_dna4_revcomp_avx2.c.o
FAILED: libavx2lib.a.p/src_dna4_revcomp_avx2.c.o 
cc -Ilibavx2lib.a.p -I. -I.. -I../include -I../bench -I../test -I../src -Xclang -fcolor-diagnostics -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=gnu11 -O3 -fPIC -O3 -mpopcnt -mavx2 -fvisibility=hidden -MD -MQ libavx2lib.a.p/src_dna4_revcomp_avx2.c.o -MF libavx2lib.a.p/src_dna4_revcomp_avx2.c.o.d -o libavx2lib.a.p/src_dna4_revcomp_avx2.c.o -c ../src/dna4_revcomp_avx2.c
cc: warning: argument unused during compilation: '-mpopcnt' [-Wunused-command-line-argument]
cc: warning: argument unused during compilation: '-mavx2' [-Wunused-command-line-argument]
In file included from ../src/dna4_revcomp_avx2.c:10:
In file included from /usr/lib/clang/10.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/10.0.1/include/xmmintrin.h:13:
/usr/lib/clang/10.0.1/include/mmintrin.h:50:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:129:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:159:12: 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);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:189:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_packuswb((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:216:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:239:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:260:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckhdq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:287:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklbw((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:310:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpcklwd((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:331:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_punpckldq((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:352:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:373:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:394:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddd((__v2si)__m1, (__v2si)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:416:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:439:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddsw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:461:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:483:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_paddusw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:504:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubb((__v8qi)__m1, (__v8qi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/clang/10.0.1/include/mmintrin.h:525:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_psubw((__v4hi)__m1, (__v4hi)__m2);
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
ninja: build stopped: subcommand failed.

dna4_revcomp performance improvement

The double shuffle method seems to be faster or at least as fast as the current method. I might want to reevaluate this for a future update.

2019 Macbook Pro (Coffee Lake i7):

---------------------------------------------------------------
Benchmark                     Time             CPU   Iterations
---------------------------------------------------------------
dnax_revcomp             397986 ns       397858 ns         1748
dnax_replace             388305 ns       388255 ns         1778
bwa_bench                 40742 ns        40726 ns        17125
bench/dna4_revcomp        72106 ns        72061 ns        12525
bench/revcomp_switch    6352159 ns      6350606 ns          109
bench/revcomp_table4     382184 ns       382081 ns         1824
bench/twiddle             44742 ns        44702 ns        15290
bench/subtract            43210 ns        43199 ns        15951
bench/twiddle_sse42       60829 ns        60799 ns        11387
bench/shuffle             42752 ns        42740 ns        16329
bench/twiddle_avx2        49461 ns        49445 ns        14284
bench/shuffle_avx2        38414 ns        38402 ns        18023

Rust wrapper

Rust is getting more and more popular in bioinformatics. Libdna already has a C and C++ API. Can libdna simply be wrapper via Rusts FFI?

Release stable version v1

Finish dna4_revcomp #2
dnax_find_first_of: man page & readthedocs
dnax_find_first_not_of: man page & readthedocs
Remove libbenchmark dependency

Publish documentation on Read the Docs

I am a friend of documentation. While libdna does not yet have as much of it as I would like to see, quite a number of functions already have manpages. As all the cool kids these days seem to use readthedocs.io we should be there, too.

Publish on readthedocs.io
Convert manpages, maybe using man-to-md.
automatic updates?

std::string::resize_and_overwrite

C++23 provides a new method resize_and_overwrite to allow access to the uninitialized bytes of the buffer. This can be used to skip the default initialisation.

Build failure on ARM

On non-x86 architectures the x86 specific implementations need to be disabled.
Courtesy to @fuzxxl.

dnax_find_first_mismatch

Provide inline version for better optimization. Beware of the difference of the inline keyword in C and C++.

Add an integer to integer hash function

I like the idea of this library very much! Great idea!

Could you please add this invertible integer to integer hash function?
See https://gist.githubusercontent.com/lh3/974ced188be2f90422cc/raw/55fbbb63e489328fd9d1641897954ca997b65951/inthash.c
and https://gist.github.com/lh3/59882d6b96166dfc3d8d

A minor nit. dna4_hash is a bit of a misnomer. Calling something a hash function usually implies that the resulting numbers are roughly distributed uniformly, even when the input data is not distributed uniformly. See https://en.wikipedia.org/wiki/Avalanche_effect. I'd be inclined to call this function dna4_pack64, that is, pack an alphabet of four nucleotides into 64 bits. That integer can then be put through the above integer to integer hash function to produce a uniformly distributed hash value.

When computing minimizers for example (as with minimap2), the result of the current dna4_hash would be a suboptimal choice for a minimizer, since it would preferentially select polyA k-mers. Mixing the bits with Thomas Wang's integer hash function produces good hash values for minimizers.

Cheers!
Shaun

dna4_fill_random

Add a function to fill a buffer with random nucleotides. Proposed API:

void dna4_fill_random(char *begin, char *end, uint32_t seed).

random string repeats after 2^30

As NOISE1 has the lowest two bits set to zero the top to bits of n get shifted out and don't affect the result. This means that the sequence repeats after 2^30 rather than 2^32. Consider setting the lowest bit to 1 to avoid this issue.

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