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forward-backward search seems working

This commit is contained in:
Heng Li 2011-10-25 12:31:36 -04:00
parent aabb807734
commit f56edd07dd
4 changed files with 13 additions and 9 deletions
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1
Makefile
View File

@ -34,6 +34,7 @@ bwt1away.o:bwt.h bwtaln.h
bwt2fmv.o:bwt.h
bntseq.o:bntseq.h
bwtgap.o:bwtgap.h bwtaln.h bwt.h
fastmap:bwt.h
bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h

13
bwt.c
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@ -249,13 +249,13 @@ void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_b
int i;
bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
for (i = 0; i != 4; ++i) {
ok[i].x[!is_back] = bwt->L2[i] + tk[i] + 1;
ok[i].x[2] = (tl[i] -= tk[i]);
ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i];
ok[i].x[2] = tl[i] - tk[i];
}
ok[3].x[is_back] = ik->x[is_back];
ok[2].x[is_back] = ok[3].x[is_back] + tl[3];
ok[1].x[is_back] = ok[2].x[is_back] + tl[2];
ok[0].x[is_back] = ok[1].x[is_back] + tl[1];
ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
}
static void bwt_reverse_intvs(bwtintv_v *p)
@ -298,7 +298,6 @@ int bwt_smem1(const bwt_t *bwt, int len, const uint8_t *q, int x, bwtintv_v *mem
ret = curr->a[0].info; // this will be the returned value
swap = curr; curr = prev; prev = swap;
if (x == 40) printf("[%lld,%lld,%lld]\n", prev->a[0].x[0], prev->a[0].x[1], prev->a[0].x[2]);
for (i = x - 1; i >= -1; --i) { // backward search for MEMs
if (q[i] > 3) break;
c = i < 0? 0 : q[i];

2
bwt.h
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@ -81,7 +81,7 @@ typedef struct { size_t n, m; bwtintv_t *a; } bwtintv_v;
(bwt)->L2[bwt_B0(bwt, k)] + bwt_occ(bwt, k, bwt_B0(bwt, k)) \
: (bwt)->L2[bwt_B0(bwt, (k)-1)] + bwt_occ(bwt, k, bwt_B0(bwt, (k)-1)))
#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)], (ik).x[2] = (bwt)->L2[(int)(c)+1] - (bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3-(c)], (ik).info = 0)
#define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)]+1, (ik).x[2] = (bwt)->L2[(int)(c)+1]-(bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3-(c)]+1, (ik).info = 0)
#ifdef __cplusplus
extern "C" {

6
fastmap.c
View File

@ -40,7 +40,9 @@ int main_fastmap(int argc, char *argv[])
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
{
int beg = 98;
int beg = 97;
uint8_t str[3];
bwtint_t b, e;
bwtintv_t ik, ok[4];
bwt_set_intv(bwt, seq->seq.s[seq->seq.l - 1], ik);
for (i = seq->seq.l - 2; i >= beg; --i) {
@ -50,6 +52,7 @@ int main_fastmap(int argc, char *argv[])
if (ik.x[2] == 0) break;
}
printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i+1);
//str[0] = '\1'; str[1] = '\3'; bwt_match_exact(bwt, 2, str, &b, &e); printf("%lld,%lld,%lld\n", b, e, e-b+1);
printf("======================== %lld, [%lld,%lld,%lld,%lld]\n", bwt->primary, bwt->L2[1], bwt->L2[2]-bwt->L2[1], bwt->L2[3]-bwt->L2[2], bwt->L2[4]-bwt->L2[3]);
bwt_set_intv(bwt, seq->seq.s[beg], ik);
for (i = beg + 1; i < seq->seq.l; ++i) {
@ -59,6 +62,7 @@ int main_fastmap(int argc, char *argv[])
if (ik.x[2] == 0) break;
}
printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i-1);
//str[0] = '\0'; str[1] = '\2'; bwt_match_exact(bwt, 2, str, &b, &e); printf("%lld,%lld,%lld\n", b, e, e-b+1);
}
bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
printf(">%s\t%ld\n", seq->name.s, mem.n);