mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
492 lines
15 KiB
C++
492 lines
15 KiB
C++
#include <stdio.h>
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#include "htab.h"
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#include "ksort.h"
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#include "Hash_Table.h"
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#define HA_KMER_GOOD_RATIO 0.333
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typedef struct { // this struct is not strictly necessary; we can use k_mer_pos instead, with modifications
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uint64_t srt;
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uint32_t self_off:31, good:1;
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uint32_t other_off;
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} anchor1_t;
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#define an_key1(a) ((a).srt)
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#define an_key2(a) ((a).self_off)
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KRADIX_SORT_INIT(ha_an1, anchor1_t, an_key1, 8)
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KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
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#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
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KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
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#define oreg_ss_lt(a, b) ((a).shared_seed > (b).shared_seed) // in the decending order
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KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)
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typedef struct {
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int n, good;
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const ha_idxpos_t *a;
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} seed1_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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ha_mz1_v mz;
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seed1_t *seed;
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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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}
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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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int ha_ov_type(const overlap_region *r, uint32_t len)
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{
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if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
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else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 3; // containing a shorter read
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else return r->x_pos_s == 0? 0 : 1;
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}
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void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain,
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kvec_t_u8_warp* k_flag, 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)
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{
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uint32_t i, rlen;
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uint64_t k, l;
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double low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
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double high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
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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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recover_UC_Read(ucr, &R_INF, rid);
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ab->mz.n = 0, ab->n_a = 0;
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rlen = Get_READ_LENGTH(R_INF, rid); // read length
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// get the list of anchors
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ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, NULL);
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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->seed[i].good = (n > low_occ && n < high_occ);
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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? ucr->length - 1 - (z->pos + 1 - z->span) : z->pos;
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an->good = s->good;
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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->good = ab->a[k].good;
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}
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cl->length = ab->n_a;
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calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
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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) {
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const overlap_region *r = &overlap_list->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)overlap_list->length; ++i) {
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overlap_region *r = &overlap_list->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 = overlap_list->list[k];
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overlap_list->list[k] = overlap_list->list[i];
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overlap_list->list[i] = t;
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}
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++k;
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}
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}
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overlap_list->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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void calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
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uint64_t readID, ma_utg_v *ua, double band_width_threshold, int add_beg_end, overlap_region* f_cigar, long long mz_occ, double mz_rate)
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{
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long long i = 0;
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uint64_t current_ID;
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uint64_t current_stand;
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if (candidates->length == 0)
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{
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return;
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}
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long long sub_region_beg;
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long long sub_region_end;
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long long chain_len;
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clear_fake_cigar(&((*f_cigar).f_cigar));
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i = 0;
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while (i < candidates->length)
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{
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chain_idx->a.n = 0;
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current_ID = candidates->list[i].readID;
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current_stand = candidates->list[i].strand;
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///reference read
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(*f_cigar).x_id = readID;
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(*f_cigar).x_pos_strand = current_stand;
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///query read
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(*f_cigar).y_id = current_ID;
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///here the strand of query is always 0
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(*f_cigar).y_pos_strand = 0;
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sub_region_beg = i;
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sub_region_end = i;
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i++;
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while (i < candidates->length
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&&
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current_ID == candidates->list[i].readID
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&&
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current_stand == candidates->list[i].strand)
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{
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sub_region_end = i;
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i++;
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}
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if ((*f_cigar).x_id == (*f_cigar).y_id)
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{
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continue;
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}
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chain_len = chain_DP(candidates->list + sub_region_beg,
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sub_region_end - sub_region_beg + 1, &(candidates->chainDP), f_cigar, band_width_threshold,
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50, ua->a[(*f_cigar).x_id].len, ua->a[(*f_cigar).y_id].len);
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// if ((*f_cigar).x_id != (*f_cigar).y_id)
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if ((*f_cigar).x_id != (*f_cigar).y_id && chain_len > mz_occ*mz_rate)
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{
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append_utg_inexact_overlap_region_alloc(overlap_list, f_cigar, ua, add_beg_end);
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}
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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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// 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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// 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->seed[i].good = 0;
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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->good = s->good;
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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->good = ab->a[k].good;
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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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#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) {
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const overlap_region *r = &overlap_list->list[i];
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w = ha_ov_type(r, u->len);
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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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for (i = 0, k = 0; i < (uint32_t)overlap_list->length; ++i) {
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overlap_region *r = &overlap_list->list[i];
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w = ha_ov_type(r, u->len);
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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 = overlap_list->list[k];
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overlap_list->list[k] = overlap_list->list[i];
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overlap_list->list[i] = t;
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}
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++k;
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}
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}
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overlap_list->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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void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
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{
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uint64_t j = 0, inner_j = 0;
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while (j < overlap_list->length && inner_j < paf->length)
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{
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if(overlap_list->list[j].y_id < paf->buffer[inner_j].tn)
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{
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j++;
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}
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else if(overlap_list->list[j].y_id > paf->buffer[inner_j].tn)
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{
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inner_j++;
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}
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else
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{
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if(overlap_list->list[j].y_pos_strand == paf->buffer[inner_j].rev)
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{
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overlap_list->list[j].is_match = 1;
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}
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j++;
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inner_j++;
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}
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}
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}
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void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
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int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf, overlap_region* f_cigar,
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kvec_t_u64_warp* dbg_ct)
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{
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extern void *ha_flt_tab;
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extern ha_pt_t *ha_idx;
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extern void *ha_flt_tab_hp;
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extern ha_pt_t *ha_idx_hp;
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ha_get_new_candidates(ab, rid, ucr, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar, dbg_ct);
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if(ha_idx_hp)
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{
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uint32_t i, k, y_id, overlapLen, max_i;
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int shared_seed;
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overlap_region t;
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overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
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ma_hit_sort_tn(paf->buffer, paf->length);
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ma_hit_sort_tn(rev_paf->buffer, rev_paf->length);
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lable_matched_ovlp(overlap_list, paf);
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lable_matched_ovlp(overlap_list, rev_paf);
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for (i = 0, k = 0; i < overlap_list->length; ++i)
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{
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if(overlap_list->list[i].is_match == 1)
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{
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if(k != i)
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{
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t = overlap_list->list[k];
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overlap_list->list[k] = overlap_list->list[i];
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overlap_list->list[i] = t;
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overlap_list->list[k].is_match = 0;
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}
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k++;
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}
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}
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overlap_list->length = k;
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ha_get_new_candidates(ab, rid, ucr, overlap_list_hp, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab_hp, ha_idx_hp, f_cigar, dbg_ct);
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if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
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{
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overlap_list->list = (overlap_region*)realloc(overlap_list->list,
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sizeof(overlap_region)*(overlap_list->length + overlap_list_hp->length));
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memset(overlap_list->list + overlap_list->size, 0, sizeof(overlap_region)*
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(overlap_list->length + overlap_list_hp->length - overlap_list->size));
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overlap_list->size = overlap_list->length + overlap_list_hp->length;
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}
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for (i = 0, k = overlap_list->length; i < overlap_list_hp->length; i++, k++)
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{
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t = overlap_list->list[k];
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overlap_list->list[k] = overlap_list_hp->list[i];
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overlap_list_hp->list[i] = t;
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}
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overlap_list->length = k;
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overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
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i = k = 0;
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while (i < overlap_list->length)
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{
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y_id = overlap_list->list[i].y_id;
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shared_seed = overlap_list->list[i].shared_seed;
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overlapLen = overlap_list->list[i].overlapLen;
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max_i = i;
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i++;
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while (i < overlap_list->length && overlap_list->list[i].y_id == y_id)
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{
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if((overlap_list->list[i].shared_seed > shared_seed) ||
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((overlap_list->list[i].shared_seed == shared_seed) && (overlap_list->list[i].overlapLen <= overlapLen)))
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{
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y_id = overlap_list->list[i].y_id;
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shared_seed = overlap_list->list[i].shared_seed;
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overlapLen = overlap_list->list[i].overlapLen;
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max_i = i;
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}
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i++;
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}
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if(k != max_i)
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{
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t = overlap_list->list[k];
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overlap_list->list[k] = overlap_list->list[max_i];
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overlap_list->list[max_i] = t;
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}
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k++;
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}
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overlap_list->length = k;
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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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void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list)
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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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