mem_opt_t *mem_opt_init() { mem_opt_t *o; o = calloc(1, sizeof(mem_opt_t)); o->flag = 0; o->a = 1; o->b = 4; o->o_del = o->o_ins = 6; o->e_del = o->e_ins = 1; o->w = 100; o->T = 30; o->zdrop = 100; o->pen_unpaired = 17; o->pen_clip5 = o->pen_clip3 = 5; o->min_seed_len = 19; o->split_width = 10; o->max_occ = 500; o->max_chain_gap = 10000; o->max_ins = 10000; o->mask_level = 0.50; o->drop_ratio = 0.50; o->XA_drop_ratio = 0.80; o->split_factor = 1.5; o->chunk_size = 10000000; o->n_threads = 1; o->max_hits = 5; o->max_matesw = 50; o->mask_level_redun = 0.95; o->min_chain_weight = 0; o->max_chain_extend = 1<<30; o->mapQ_coef_len = 50; o->mapQ_coef_fac = log(o->mapQ_coef_len); bwa_fill_scmat(o->a, o->b, o->mat); return o; }
void bsw2_extend_rght(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem) { int i; bwtint_t k; uint8_t *target; int8_t mat[25]; bwa_fill_scmat(opt->a, opt->b, mat); target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1); for (i = 0; i < b->n; ++i) { bsw2hit_t *p = b->hits + i; int lt = ((lq - p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq; int j, score, qle, tle; if (p->l) continue; for (k = p->k, j = 0; k < p->k + lt && k < l_pac; ++k) target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3; lt = j; score = ksw_extend(lq - p->beg, &query[p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, 1, &qle, &tle, 0, 0, 0) - 1; // if (score < p->G) fprintf(stderr, "[bsw2_extend_hits] %d < %d\n", score, p->G); if (score >= p->G) { p->G = score; p->len = tle; p->end = p->beg + qle; } } free(target); }
void bsw2_extend_left(const bsw2opt_t *opt, bwtsw2_t *b, uint8_t *_query, int lq, uint8_t *pac, bwtint_t l_pac, uint8_t *_mem) { int i; bwtint_t k; uint8_t *target = 0, *query; int8_t mat[25]; bwa_fill_scmat(opt->a, opt->b, mat); query = calloc(lq, 1); // sort according to the descending order of query end ks_introsort(hit, b->n, b->hits); target = calloc(((lq + 1) / 2 * opt->a + opt->r) / opt->r + lq, 1); // reverse _query for (i = 0; i < lq; ++i) query[lq - i - 1] = _query[i]; // core loop for (i = 0; i < b->n; ++i) { bsw2hit_t *p = b->hits + i; int lt = ((p->beg + 1) / 2 * opt->a + opt->r) / opt->r + lq; int score, j, qle, tle; p->n_seeds = 1; if (p->l || p->k == 0) continue; for (j = score = 0; j < i; ++j) { bsw2hit_t *q = b->hits + j; if (q->beg <= p->beg && q->k <= p->k && q->k + q->len >= p->k + p->len) { if (q->n_seeds < (1<<13) - 2) ++q->n_seeds; ++score; } } if (score) continue; if (lt > p->k) lt = p->k; for (k = p->k - 1, j = 0; k > 0 && j < lt; --k) // FIXME: k=0 not considered! target[j++] = pac[k>>2] >> (~k&3)*2 & 0x3; lt = j; score = ksw_extend(p->beg, &query[lq - p->beg], lt, target, 5, mat, opt->q, opt->r, opt->bw, 0, -1, p->G, &qle, &tle, 0, 0, 0); if (score > p->G) { // extensible p->G = score; p->k -= tle; p->len += tle; p->beg -= qle; } } free(query); free(target); }
/* generate CIGAR array(s) in b->cigar[] */ static void gen_cigar(const bsw2opt_t *opt, int lq, uint8_t *seq[2], int64_t l_pac, const uint8_t *pac, bwtsw2_t *b, const char *name) { int i; int8_t mat[25]; bwa_fill_scmat(opt->a, opt->b, mat); for (i = 0; i < b->n; ++i) { bsw2hit_t *p = b->hits + i; bsw2aux_t *q = b->aux + i; uint8_t *query; int beg, end, score; if (p->l) continue; beg = (p->flag & 0x10)? lq - p->end : p->beg; end = (p->flag & 0x10)? lq - p->beg : p->end; query = seq[(p->flag & 0x10)? 1 : 0] + beg; q->cigar = bwa_gen_cigar(mat, opt->q, opt->r, opt->bw, l_pac, pac, end - beg, query, p->k, p->k + p->len, &score, &q->n_cigar, &q->nm); #if 0 if (name && score != p->G) { // debugging only int j, glen = 0; for (j = 0; j < q->n_cigar; ++j) if ((q->cigar[j]&0xf) == 1 || (q->cigar[j]&0xf) == 2) glen += q->cigar[j]>>4; fprintf(stderr, "[E::%s] %s - unequal score: %d != %d; (qlen, aqlen, arlen, glen, bw) = (%d, %d, %d, %d, %d)\n", __func__, name, score, p->G, lq, end - beg, p->len, glen, opt->bw); } #endif if (q->cigar && (beg != 0 || end < lq)) { // write soft clipping q->cigar = realloc(q->cigar, 4 * (q->n_cigar + 2)); if (beg != 0) { memmove(q->cigar + 1, q->cigar, q->n_cigar * 4); q->cigar[0] = beg<<4 | 4; ++q->n_cigar; } if (end < lq) { q->cigar[q->n_cigar] = (lq - end)<<4 | 4; ++q->n_cigar; } } }