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perhaps improves samse/sampe

This commit is contained in:
Heng Li 2011-11-24 01:22:02 -05:00
parent 196b50dde3
commit eeedda105d
1 changed files with 5 additions and 2 deletions
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7
bwt.c
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@ -49,7 +49,10 @@ void bwt_gen_cnt_table(bwt_t *bwt)
void bwt_cal_sa(bwt_t *bwt, int intv) void bwt_cal_sa(bwt_t *bwt, int intv)
{ {
bwtint_t isa, sa, i; // S(isa) = sa bwtint_t isa, sa, i; // S(isa) = sa
int intv_round = intv;
kv_roundup32(intv_round);
xassert(intv_round == intv, "SA sample interval is not a power of 2.");
xassert(bwt->bwt, "bwt_t::bwt is not initialized."); xassert(bwt->bwt, "bwt_t::bwt is not initialized.");
if (bwt->sa) free(bwt->sa); if (bwt->sa) free(bwt->sa);
@ -73,8 +76,8 @@ void bwt_cal_sa(bwt_t *bwt, int intv)
bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k) bwtint_t bwt_sa(const bwt_t *bwt, bwtint_t k)
{ {
bwtint_t sa = 0; bwtint_t sa = 0, mask = bwt->sa_intv - 1;
while (k % bwt->sa_intv != 0) { while (k & mask) {
++sa; ++sa;
k = bwt_invPsi(bwt, k); k = bwt_invPsi(bwt, k);
} }