zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

code backup: less dependent on gcc optimization

This commit is contained in:
Heng Li 2013-02-26 11:14:19 -05:00
parent e70c7c2a71
commit 174fe0f1d5
2 changed files with 14 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
bwt.c
View File

@ -161,7 +161,7 @@ void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok,
void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4]) void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
{ {
bwtint_t l, j, x; bwtint_t l, j, x;
uint32_t *p; uint32_t *p, tmp;
if (k == (bwtint_t)(-1)) { if (k == (bwtint_t)(-1)) {
memset(cnt, 0, 4 * sizeof(bwtint_t)); memset(cnt, 0, 4 * sizeof(bwtint_t));
return; return;
@ -171,9 +171,10 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
memcpy(cnt, p, 4 * sizeof(bwtint_t)); memcpy(cnt, p, 4 * sizeof(bwtint_t));
p += sizeof(bwtint_t); p += sizeof(bwtint_t);
j = k >> 4 << 4; j = k >> 4 << 4;
for (l = k / OCC_INTERVAL * OCC_INTERVAL, x = 0; l < j; l += 16, ++p) for (l = k & ~OCC_INTV_MASK, x = 0; l < j; l += 16, ++p)
x += __occ_aux4(bwt, *p); x += __occ_aux4(bwt, *p);
x += __occ_aux4(bwt, *p & ~((1U<<((~k&15)<<1)) - 1)) - (~k&15); tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
x += __occ_aux4(bwt, tmp) - (~k&15);
cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24; cnt[0] += x&0xff; cnt[1] += x>>8&0xff; cnt[2] += x>>16&0xff; cnt[3] += x>>24;
} }
@ -188,7 +189,7 @@ void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtin
bwt_occ4(bwt, l, cntl); bwt_occ4(bwt, l, cntl);
} else { } else {
bwtint_t i, j, x, y; bwtint_t i, j, x, y;
uint32_t *p; uint32_t *p, tmp;
if (k >= bwt->primary) --k; // because $ is not in bwt if (k >= bwt->primary) --k; // because $ is not in bwt
if (l >= bwt->primary) --l; if (l >= bwt->primary) --l;
p = bwt_occ_intv(bwt, k); p = bwt_occ_intv(bwt, k);
@ -196,14 +197,16 @@ void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtin
p += sizeof(bwtint_t); p += sizeof(bwtint_t);
// prepare cntk[] // prepare cntk[]
j = k >> 4 << 4; j = k >> 4 << 4;
for (i = k / OCC_INTERVAL * OCC_INTERVAL, x = 0; i < j; i += 16, ++p) for (i = k & ~OCC_INTV_MASK, x = 0; i < j; i += 16, ++p)
x += __occ_aux4(bwt, *p); x += __occ_aux4(bwt, *p);
y = x; y = x;
x += __occ_aux4(bwt, *p & ~((1U<<((~k&15)<<1)) - 1)) - (~k&15); tmp = *p & ~((1U<<((~k&15)<<1)) - 1);
x += __occ_aux4(bwt, tmp) - (~k&15);
// calculate cntl[] and finalize cntk[] // calculate cntl[] and finalize cntk[]
j = l >> 4 << 4; j = l >> 4 << 4;
for (; i < j; i += 16, ++p) y += __occ_aux4(bwt, *p); for (; i < j; i += 16, ++p) y += __occ_aux4(bwt, *p);
y += __occ_aux4(bwt, *p & ~((1U<<((~l&15)<<1)) - 1)) - (~l&15); tmp = *p & ~((1U<<((~l&15)<<1)) - 1);
y += __occ_aux4(bwt, tmp) - (~l&15);
memcpy(cntl, cntk, 4 * sizeof(bwtint_t)); memcpy(cntl, cntk, 4 * sizeof(bwtint_t));
cntk[0] += x&0xff; cntk[1] += x>>8&0xff; cntk[2] += x>>16&0xff; cntk[3] += x>>24; cntk[0] += x&0xff; cntk[1] += x>>8&0xff; cntk[2] += x>>16&0xff; cntk[3] += x>>24;
cntl[0] += y&0xff; cntl[1] += y>>8&0xff; cntl[2] += y>>16&0xff; cntl[3] += y>>24; cntl[0] += y&0xff; cntl[1] += y>>8&0xff; cntl[2] += y>>16&0xff; cntl[3] += y>>24;

6
bwt.h
View File

@ -30,8 +30,10 @@
#include <stdint.h> #include <stdint.h>
// requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line // requirement: (OCC_INTERVAL%16 == 0); please DO NOT change this line because some part of the code assume OCC_INTERVAL=0x80
#define OCC_INTERVAL 0x80 #define OCC_INTV_SHIFT 7
#define OCC_INTERVAL (1LL<<OCC_INTV_SHIFT)
#define OCC_INTV_MASK (OCC_INTERVAL - 1)
#ifndef BWA_UBYTE #ifndef BWA_UBYTE
#define BWA_UBYTE #define BWA_UBYTE