diff --git a/fastmap.c b/fastmap.c index de5bc0d..ee8e9b4 100644 --- a/fastmap.c +++ b/fastmap.c @@ -39,31 +39,6 @@ int main_fastmap(int argc, char *argv[]) while (kseq_read(seq) >= 0) { for (i = 0; i < seq->seq.l; ++i) seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]]; - { - 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) { - //printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i+1); - bwt_extend(bwt, &ik, ok, 1); - ik = ok[seq->seq.s[i]]; - 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) { - //printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i-1); - bwt_extend(bwt, &ik, ok, 0); - ik = ok[3-seq->seq.s[i]]; - 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); for (i = 0; i < mem.n; ++i) {