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performance increase in alignment #279

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performance increase in alignment #279

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24 changes: 20 additions & 4 deletions bwt.c
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Original file line number Diff line number Diff line change
Expand Up @@ -95,7 +95,7 @@ bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
return sa + bwt->sa[k/bwt->sa_intv];
}

static inline int __occ_aux(uint64_t y, int c)
static inline int __occ_aux_old(uint64_t y, int c)
{
// reduce nucleotide counting to bits counting
y = ((c&2)? y : ~y) >> 1 & ((c&1)? y : ~y) & 0x5555555555555555ull;
Expand All @@ -104,6 +104,22 @@ static inline int __occ_aux(uint64_t y, int c)
return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
}

static inline int __occ_aux(uint64_t y, int c){
switch(c){
case 0:
return __occ_aux_old(y, 0);
case 1:
return __occ_aux_old(y, 1);
case 2:
return __occ_aux_old(y, 2);
case 3:
return __occ_aux_old(y, 3);
default:
return __occ_aux_old(y, c);
}
}


bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
{
bwtint_t n;
Expand All @@ -119,7 +135,7 @@ bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)

// calculate Occ up to the last k/32
end = p + (((k>>5) - ((k&~OCC_INTV_MASK)>>5))<<1);
for (; p < end; p += 2) n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
for (; p < end; p += 2) n += __occ_aux(*((uint64_t*)p), c);
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// calculate Occ
n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
Expand Down Expand Up @@ -147,15 +163,15 @@ void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok,
// calculate *ok
j = k >> 5 << 5;
for (i = k/OCC_INTERVAL*OCC_INTERVAL; i < j; i += 32, p += 2)
n += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
n += __occ_aux(*((uint64_t*)p), c);
m = n;
n += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~k&31)<<1)) - 1), c);
if (c == 0) n -= ~k&31; // corrected for the masked bits
*ok = n;
// calculate *ol
j = l >> 5 << 5;
for (; i < j; i += 32, p += 2)
m += __occ_aux((uint64_t)p[0]<<32 | p[1], c);
m += __occ_aux(*((uint64_t*)p), c);
m += __occ_aux(((uint64_t)p[0]<<32 | p[1]) & ~((1ull<<((~l&31)<<1)) - 1), c);
if (c == 0) m -= ~l&31; // corrected for the masked bits
*ol = m;
Expand Down