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

code backup

This commit is contained in:
Heng Li 2013-02-26 11:22:24 -05:00
parent 174fe0f1d5
commit c848b44481
1 changed files with 6 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
bwt.c
View File

@ -166,7 +166,7 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
memset(cnt, 0, 4 * sizeof(bwtint_t)); memset(cnt, 0, 4 * sizeof(bwtint_t));
return; return;
} }
if (k >= bwt->primary) --k; // because $ is not in bwt k -= (k >= bwt->primary); // because $ is not in bwt
p = bwt_occ_intv(bwt, k); p = bwt_occ_intv(bwt, k);
memcpy(cnt, p, 4 * sizeof(bwtint_t)); memcpy(cnt, p, 4 * sizeof(bwtint_t));
p += sizeof(bwtint_t); p += sizeof(bwtint_t);
@ -182,16 +182,16 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
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 - (k >= bwt->primary);
_l = (l >= bwt->primary)? l-1 : l; _l = l - (l >= bwt->primary);
if (_l/OCC_INTERVAL != _k/OCC_INTERVAL || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) { if (_l>>OCC_INTV_SHIFT != _k>>OCC_INTV_SHIFT || k == (bwtint_t)(-1) || l == (bwtint_t)(-1)) {
bwt_occ4(bwt, k, cntk); bwt_occ4(bwt, k, cntk);
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, tmp; uint32_t *p, tmp;
if (k >= bwt->primary) --k; // because $ is not in bwt k -= (k >= bwt->primary); // because $ is not in bwt
if (l >= bwt->primary) --l; l -= (l >= bwt->primary);
p = bwt_occ_intv(bwt, k); p = bwt_occ_intv(bwt, k);
memcpy(cntk, p, 4 * sizeof(bwtint_t)); memcpy(cntk, p, 4 * sizeof(bwtint_t));
p += sizeof(bwtint_t); p += sizeof(bwtint_t);