15, 14, 13, 12));
/* The bits have now been shifted to the right locations;
* translate their values 0..63 to the Base64 alphabet.
* Because AVX2 can only compare 'greater than', start from end of alphabet: */
/* set 5: 63, "/" */
s5mask = _mm256_cmpeq_epi8(res, _mm256_set1_epi8(63));
blockmask = s5mask;
/* set 4: 62, "+" */
s4mask = _mm256_cmpeq_epi8(res, _mm256_set1_epi8(62));
blockmask = _mm256_or_si256(blockmask, s4mask);
/* set 3: 52..61, "0123456789" */
s3mask = _mm256_andnot_si256(blockmask, _mm256_cmpgt_epi8(res, _mm256_set1_epi8(51)));
blockmask = _mm256_or_si256(blockmask, s3mask);
/* set 2: 26..51, "abcdefghijklmnopqrstuvwxyz" */
s2mask = _mm256_andnot_si256(blockmask, _mm256_cmpgt_epi8(res, _mm256_set1_epi8(25)));
blockmask = _mm256_or_si256(blockmask, s2mask);
/* set 1: 0..25, "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
* Everything that is not blockmasked */
/* Create the masked character sets: */
str = _mm256_and_si256(_mm256_set1_epi8('/'), s5mask);
str = _mm256_blendv_epi8(str, _mm256_set1_epi8('+'), s4mask);
str = _mm256_blendv_epi8(str, _mm256_add_epi8(res, _mm256_set1_epi8('0' - 52)), s3mask);
str = _mm256_blendv_epi8(str, _mm256_add_epi8(res, _mm256_set1_epi8('a' - 26)), s2mask);
str = _mm256_blendv_epi8(_mm256_add_epi8(res, _mm256_set1_epi8('A')), str, blockmask);
__m256i test_mm256_cmpgt_epi8(__m256i a, __m256i b) {
// CHECK: icmp sgt <32 x i8>
return _mm256_cmpgt_epi8(a, b);
}
// count genotype sum and number of calls, not requiring 16-aligned p
COREARRAY_DLL_DEFAULT C_UInt8* vec_u8_geno_count(C_UInt8 *p,
size_t n, C_Int32 &out_sum, C_Int32 &out_num)
{
C_Int32 sum=0, num=0;
#if defined(COREARRAY_SIMD_AVX2)
const __m256i three = _mm256_set1_epi8(3);
const __m256i zero = _mm256_setzero_si256();
__m256i sum32 = zero, num32 = zero;
size_t limit_by_U8 = 0;
for (; n >= 32; )
{
__m256i v = _mm256_loadu_si256((__m256i const*)p);
p += 32;
__m256i m = _mm256_cmpgt_epi8(three, _mm256_min_epu8(v, three));
sum32 = _mm256_add_epi8(sum32, _mm256_and_si256(v, m));
num32 = _mm256_sub_epi8(num32, m);
n -= 32;
limit_by_U8 ++;
if ((limit_by_U8 >= 127) || (n < 32))
{
// add to sum
sum32 = _mm256_sad_epu8(sum32, zero);
sum32 = _mm256_add_epi32(sum32,
_mm256_permute4x64_epi64(sum32, _MM_SHUFFLE(1,0,3,2)));
sum32 = _mm256_add_epi32(sum32,
_mm256_permute4x64_epi64(sum32, _MM_SHUFFLE(0,0,0,1)));
sum += _mm_cvtsi128_si32(_mm256_castsi256_si128(sum32));
// add to num
num32 = _mm256_sad_epu8(num32, zero);
num32 = _mm256_add_epi32(num32,
_mm256_permute4x64_epi64(num32, _MM_SHUFFLE(1,0,3,2)));
num32 = _mm256_add_epi32(num32,
_mm256_permute4x64_epi64(num32, _MM_SHUFFLE(0,0,0,1)));
num += _mm_cvtsi128_si32(_mm256_castsi256_si128(num32));
// reset
sum32 = num32 = zero;
limit_by_U8 = 0;
}
}
#elif defined(COREARRAY_SIMD_SSE2)
// header, 16-byte aligned
size_t h = (16 - ((size_t)p & 0x0F)) & 0x0F;
for (; (n > 0) && (h > 0); n--, h--, p++)
if (*p <= 2) { sum += *p; num++; }
const __m128i three = _mm_set1_epi8(3);
const __m128i zero = _mm_setzero_si128();
__m128i sum16=zero, num16=zero;
size_t limit_by_U8 = 0;
for (; n >= 16; )
{
__m128i v = _mm_load_si128((__m128i const*)p);
p += 16;
__m128i m = _mm_cmpgt_epi8(three, _mm_min_epu8(v, three));
sum16 = _mm_add_epi8(sum16, v & m);
num16 = _mm_sub_epi8(num16, m);
n -= 16;
limit_by_U8 ++;
if ((limit_by_U8 >= 127) || (n < 16))
{
// add to sum
sum16 = _mm_sad_epu8(sum16, zero);
sum += _mm_cvtsi128_si32(sum16);
sum += _mm_cvtsi128_si32(_mm_shuffle_epi32(sum16, 2));
// add to num
num16 = _mm_sad_epu8(num16, zero);
num += _mm_cvtsi128_si32(num16);
num += _mm_cvtsi128_si32(_mm_shuffle_epi32(num16, 2));
// reset
sum16 = num16 = zero;
limit_by_U8 = 0;
}
}
#endif
for (; n > 0; n--, p++)
if (*p <= 2) { sum += *p; num++; }
out_sum = sum;
out_num = num;
return p;
}
