Lines Matching refs:ksq
571 kseq_t *kst, *ksq; in main() local
600 fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq); in main()
602 while (kseq_read(ksq) > 0) { in main()
605 for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]]; in main()
607 if ((int)ksq->seq.m > max_rseq) { in main()
608 max_rseq = ksq->seq.m; in main()
611 for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j) in main()
612 rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i]; in main()
617 …r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, ga… in main()
619 …printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+… in main()
621 …r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]); in main()
623 …%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ks… in main()
630 kseq_destroy(ksq); gzclose(fpq); in main()