mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-05 20:18:11 +08:00
mempcpy -> memcpy
This commit is contained in:
chhylp123
+246
-112
@@ -29,6 +29,11 @@ typedef struct {
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const ha_idxpos_t *a;
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} seed1_t;
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typedef struct {
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int n, cnt;
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const ha_idxposl_t *a;
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} seedl_t;
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struct ha_abuf_s {
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uint64_t n_a, m_a;///number of anchors (seed positions)
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uint32_t old_mz_m;///number of seeds
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@@ -37,20 +42,23 @@ struct ha_abuf_s {
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anchor1_t *a;
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};
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ha_abuf_t *ha_abuf_init(void)
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{
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return (ha_abuf_t*)calloc(1, sizeof(ha_abuf_t));
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struct ha_abufl_s {
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uint64_t n_a, m_a;///number of anchors (seed positions)
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uint32_t old_mz_m;///number of seeds
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ha_mzl_v mz;
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seedl_t *seed;
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anchor1_t *a;
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};
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#define HA_ABUF_INIT(HType, MZType, SDType, sf) \
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HType *sf##_init(void){return (HType*)calloc(1, sizeof(HType));}\
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void sf##_destroy(HType *ab){if(ab){free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);}}\
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uint64_t sf##_mem(const HType *ab){\
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return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(MZType) + sizeof(SDType)) + sizeof(HType);\
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}
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void ha_abuf_destroy(ha_abuf_t *ab)
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{
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free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);
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}
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uint64_t ha_abuf_mem(const ha_abuf_t *ab)
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{
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return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(ha_mz1_t) + sizeof(seed1_t)) + sizeof(ha_abuf_t);
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}
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HA_ABUF_INIT(ha_abuf_s, ha_mz1_t, seed1_t, ha_abuf)
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HA_ABUF_INIT(ha_abufl_s, ha_mzl_t, seedl_t, ha_abufl)
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int ha_ov_type(const overlap_region *r, uint32_t len)
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{
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@@ -257,122 +265,248 @@ void calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* ov
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}
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}
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/**
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void ha_get_inter_candidates(ha_abufl_t *ab, int64_t uid, ma_utg_v *ua, overlap_region_alloc *ovlp,
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Candidates_list *cl, double bw_thres, int max_n_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx,
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void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp,
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double chain_match_rate, uint32_t uk, uint32_t uw, uint32_t is_hpc, uint32_t h_occ)
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{
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uint32_t i, rlen;
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uint64_t k, l;
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ma_utg_t *u = &(ua->a[uid]);
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// prepare
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clear_Candidates_list(cl);
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clear_overlap_region_alloc(ovlp);
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ab->mz.n = 0, ab->n_a = 0;
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mz2_ha_sketch(u->s, u->len, uw, uk, uid, is_hpc, &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct,
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NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 1);
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// minimizer of queried read
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if (ab->mz.m > ab->old_mz_m) {
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ab->old_mz_m = ab->mz.m;
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REALLOC(ab->seed, ab->old_mz_m);
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}
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for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
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int n;
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ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
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ab->seed[i].n = n;
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ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x);
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ab->n_a += n;
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}
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if (ab->n_a > ab->m_a) {
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ab->m_a = ab->n_a;
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kroundup64(ab->m_a);
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REALLOC(ab->a, ab->m_a);
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}
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for (i = 0, k = 0; i < ab->mz.n; ++i) {
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int j;
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///z is one of the minimizer
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ha_mzl_t *z = &ab->mz.a[i];
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seedl_t *s = &ab->seed[i];
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for (j = 0; j < s->n; ++j) {
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const ha_idxposl_t *y = &s->a[j];
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anchor1_t *an = &ab->a[k++];
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uint8_t rev = z->rev == y->rev? 0 : 1;
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an->other_off = y->pos;
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an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos;
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an->cnt = s->cnt;
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an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
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}
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}
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// sort anchors
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radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
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for (k = 1, l = 0; k <= ab->n_a; ++k) {
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if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
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if (k - l > 1)
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radix_sort_ha_an2(ab->a + l, ab->a + k);
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l = k;
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}
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}
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// copy over to _cl_
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if (ab->m_a >= (uint64_t)cl->size) {
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cl->size = ab->m_a;
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REALLOC(cl->list, cl->size);
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}
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for (k = 0; k < ab->n_a; ++k) {
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k_mer_hit *p = &cl->list[k];
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p->readID = ab->a[k].srt >> 33;
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p->strand = ab->a[k].srt >> 32 & 1;
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p->offset = ab->a[k].other_off;
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p->self_offset = ab->a[k].self_off;
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p->cnt = (ab->a[k].cnt == 1? 1 : 16);
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}
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cl->length = ab->n_a;
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// calculate_overlap_region_by_chaining(cl, ovlp, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
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// calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
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#if 0
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if (overlap_list->length > 0) {
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fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen);
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for (int i = 0; i < (int)overlap_list->length; ++i) {
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overlap_region *r = &overlap_list->list[i];
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fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
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(int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, ha_ov_type(r, rlen));
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}
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}
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#endif
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if ((int)ovlp->length > max_n_chain) {
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int32_t w, n[4], s[4];
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n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
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ks_introsort_or_ss(ovlp->length, ovlp->list);
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for (i = 0; i < (uint32_t)ovlp->length; ++i) {
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const overlap_region *r = &ovlp->list[i];
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w = ha_ov_type(r, rlen);
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++n[w];
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if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
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}
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if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
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// n[0] = n[1] = n[2] = n[3] = 0;
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for (i = 0, k = 0; i < (uint32_t)ovlp->length; ++i) {
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overlap_region *r = &ovlp->list[i];
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w = ha_ov_type(r, rlen);
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// ++n[w];
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// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
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if (r->shared_seed >= s[w]) {
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if ((uint32_t)k != i) {
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overlap_region t;
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t = ovlp->list[k];
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ovlp->list[k] = ovlp->list[i];
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ovlp->list[i] = t;
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}
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++k;
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}
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}
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ovlp->length = k;
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}
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}
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///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
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}
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**/
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void ha_get_ug_candidates(ha_abuf_t *ab, int64_t rid, ma_utg_t *u, ma_utg_v *ua, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag,
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kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, double chain_match_rate)
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{
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uint32_t i;
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uint64_t k, l;
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uint32_t i;
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uint64_t k, l;
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// prepare
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// prepare
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clear_Candidates_list(cl);
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clear_overlap_region_alloc(overlap_list);
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ab->mz.n = 0, ab->n_a = 0;
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ab->mz.n = 0, ab->n_a = 0;
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// get the list of anchors
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//should use the new version...
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///ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
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// minimizer of queried read
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if (ab->mz.m > ab->old_mz_m) {
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ab->old_mz_m = ab->mz.m;
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REALLOC(ab->seed, ab->old_mz_m);
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}
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for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
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int n;
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ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &n);
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ab->seed[i].n = n;
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ab->n_a += n;
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}
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if (ab->n_a > ab->m_a) {
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ab->m_a = ab->n_a;
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kroundup64(ab->m_a);
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REALLOC(ab->a, ab->m_a);
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}
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for (i = 0, k = 0; i < ab->mz.n; ++i) {
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int j;
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///z is one of the minimizer
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ha_mz1_t *z = &ab->mz.a[i];
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seed1_t *s = &ab->seed[i];
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for (j = 0; j < s->n; ++j) {
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const ha_idxpos_t *y = &s->a[j];
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anchor1_t *an = &ab->a[k++];
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uint8_t rev = z->rev == y->rev? 0 : 1;
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an->other_off = y->pos;
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an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos;
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an->cnt = 1;
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an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
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}
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}
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// get the list of anchors
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//should use the new version...
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///ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
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// minimizer of queried read
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if (ab->mz.m > ab->old_mz_m) {
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ab->old_mz_m = ab->mz.m;
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REALLOC(ab->seed, ab->old_mz_m);
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}
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for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
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int n;
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ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &n);
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ab->seed[i].n = n;
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ab->n_a += n;
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}
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if (ab->n_a > ab->m_a) {
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ab->m_a = ab->n_a;
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kroundup64(ab->m_a);
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REALLOC(ab->a, ab->m_a);
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}
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for (i = 0, k = 0; i < ab->mz.n; ++i) {
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int j;
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///z is one of the minimizer
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ha_mz1_t *z = &ab->mz.a[i];
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seed1_t *s = &ab->seed[i];
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for (j = 0; j < s->n; ++j) {
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const ha_idxpos_t *y = &s->a[j];
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anchor1_t *an = &ab->a[k++];
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uint8_t rev = z->rev == y->rev? 0 : 1;
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an->other_off = y->pos;
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an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos;
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an->cnt = 1;
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an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
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}
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}
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// sort anchors
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radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
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for (k = 1, l = 0; k <= ab->n_a; ++k) {
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if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
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if (k - l > 1)
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radix_sort_ha_an2(ab->a + l, ab->a + k);
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l = k;
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}
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}
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// sort anchors
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radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
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for (k = 1, l = 0; k <= ab->n_a; ++k) {
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if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
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if (k - l > 1)
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radix_sort_ha_an2(ab->a + l, ab->a + k);
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l = k;
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}
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}
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// copy over to _cl_
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if (ab->m_a >= (uint64_t)cl->size) {
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cl->size = ab->m_a;
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REALLOC(cl->list, cl->size);
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}
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for (k = 0; k < ab->n_a; ++k) {
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k_mer_hit *p = &cl->list[k];
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p->readID = ab->a[k].srt >> 33;
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p->strand = ab->a[k].srt >> 32 & 1;
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p->offset = ab->a[k].other_off;
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p->self_offset = ab->a[k].self_off;
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p->cnt = 1;
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}
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cl->length = ab->n_a;
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// copy over to _cl_
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if (ab->m_a >= (uint64_t)cl->size) {
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cl->size = ab->m_a;
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REALLOC(cl->list, cl->size);
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}
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for (k = 0; k < ab->n_a; ++k) {
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k_mer_hit *p = &cl->list[k];
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p->readID = ab->a[k].srt >> 33;
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p->strand = ab->a[k].srt >> 32 & 1;
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p->offset = ab->a[k].other_off;
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p->self_offset = ab->a[k].self_off;
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p->cnt = 1;
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}
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cl->length = ab->n_a;
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calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
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calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
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#if 0
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if (overlap_list->length > 0) {
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fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen);
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for (int i = 0; i < (int)overlap_list->length; ++i) {
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overlap_region *r = &overlap_list->list[i];
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fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
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(int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, ha_ov_type(r, rlen));
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}
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}
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#endif
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#if 0
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if (overlap_list->length > 0) {
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fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen);
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for (int i = 0; i < (int)overlap_list->length; ++i) {
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overlap_region *r = &overlap_list->list[i];
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fprintf(stderr, "C\t%d\t%d\t%d\t%c\t%d\t%ld\t%d\t%d\t%c\t%d\t%d\n", (int)r->x_id, (int)r->x_pos_s, (int)r->x_pos_e, "+-"[r->x_pos_strand],
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(int)r->y_id, (long)Get_READ_LENGTH(R_INF, r->y_id), (int)r->y_pos_s, (int)r->y_pos_e, "+-"[r->y_pos_strand], (int)r->shared_seed, ha_ov_type(r, rlen));
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}
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}
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#endif
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if ((int)overlap_list->length > max_n_chain) {
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int32_t w, n[4], s[4];
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n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
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ks_introsort_or_ss(overlap_list->length, overlap_list->list);
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for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
|
||||
const overlap_region *r = &overlap_list->list[i];
|
||||
w = ha_ov_type(r, u->len);
|
||||
++n[w];
|
||||
if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
|
||||
}
|
||||
if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
|
||||
for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
|
||||
overlap_region *r = &overlap_list->list[i];
|
||||
w = ha_ov_type(r, u->len);
|
||||
if (r->shared_seed >= s[w]) {
|
||||
if ((uint32_t)k != i) {
|
||||
overlap_region t;
|
||||
t = overlap_list->list[k];
|
||||
overlap_list->list[k] = overlap_list->list[i];
|
||||
overlap_list->list[i] = t;
|
||||
}
|
||||
++k;
|
||||
}
|
||||
}
|
||||
overlap_list->length = k;
|
||||
}
|
||||
}
|
||||
if ((int)overlap_list->length > max_n_chain) {
|
||||
int32_t w, n[4], s[4];
|
||||
n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
|
||||
ks_introsort_or_ss(overlap_list->length, overlap_list->list);
|
||||
for (i = 0; i < (uint32_t)overlap_list->length; ++i) {
|
||||
const overlap_region *r = &overlap_list->list[i];
|
||||
w = ha_ov_type(r, u->len);
|
||||
++n[w];
|
||||
if ((int)n[w] == max_n_chain) s[w] = r->shared_seed;
|
||||
}
|
||||
if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
|
||||
for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
|
||||
overlap_region *r = &overlap_list->list[i];
|
||||
w = ha_ov_type(r, u->len);
|
||||
if (r->shared_seed >= s[w]) {
|
||||
if ((uint32_t)k != i) {
|
||||
overlap_region t;
|
||||
t = overlap_list->list[k];
|
||||
overlap_list->list[k] = overlap_list->list[i];
|
||||
overlap_list->list[i] = t;
|
||||
}
|
||||
++k;
|
||||
}
|
||||
}
|
||||
overlap_list->length = k;
|
||||
}
|
||||
}
|
||||
|
||||
///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
||||
///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
||||
}
|
||||
|
||||
|
||||
void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
|
||||
{
|
||||
uint64_t j = 0, inner_j = 0;
|
||||
|
||||
Reference in New Issue
Block a user