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Merge branch 'master' of github.com:lh3/bwa

This commit is contained in:
Heng Li 2012-06-28 14:51:51 -04:00
parent f44edd4fc9 f89649ee26
commit fa51f029b9
2 changed files with 6 additions and 6 deletions
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8
bwt.c
View File

@ -95,7 +95,7 @@ static inline int __occ_aux(uint64_t y, int c)
return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56; return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
} }
inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c) bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
{ {
bwtint_t n, l, j; bwtint_t n, l, j;
uint32_t *p; uint32_t *p;
@ -121,7 +121,7 @@ inline bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, ubyte_t c)
} }
// an analogy to bwt_occ() but more efficient, requiring k <= l // an analogy to bwt_occ() but more efficient, requiring k <= l
inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol) void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol)
{ {
bwtint_t _k, _l; bwtint_t _k, _l;
_k = (k >= bwt->primary)? k-1 : k; _k = (k >= bwt->primary)? k-1 : k;
@ -158,7 +158,7 @@ inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint
((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff] \ ((bwt)->cnt_table[(b)&0xff] + (bwt)->cnt_table[(b)>>8&0xff] \
+ (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24]) + (bwt)->cnt_table[(b)>>16&0xff] + (bwt)->cnt_table[(b)>>24])
inline 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;
@ -178,7 +178,7 @@ inline void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
} }
// an analogy to bwt_occ4() but more efficient, requiring k <= l // an analogy to bwt_occ4() but more efficient, requiring k <= l
inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]) void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
{ {
bwtint_t _k, _l; bwtint_t _k, _l;
_k = (k >= bwt->primary)? k-1 : k; _k = (k >= bwt->primary)? k-1 : k;

4
bwt_lite.c
View File

@ -65,7 +65,7 @@ inline uint32_t bwtl_occ(const bwtl_t *bwt, uint32_t k, uint8_t c)
if (c == 0) n -= 15 - (k&15); // corrected for the masked bits if (c == 0) n -= 15 - (k&15); // corrected for the masked bits
return n; return n;
} }
inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4]) void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
{ {
uint32_t x, b; uint32_t x, b;
if (k == (uint32_t)(-1)) { if (k == (uint32_t)(-1)) {
@ -80,7 +80,7 @@ inline void bwtl_occ4(const bwtl_t *bwt, uint32_t k, uint32_t cnt[4])
x -= 15 - (k&15); x -= 15 - (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;
} }
inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]) void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4])
{ {
bwtl_occ4(bwt, k, cntk); bwtl_occ4(bwt, k, cntk);
bwtl_occ4(bwt, l, cntl); bwtl_occ4(bwt, l, cntl);