mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-09-15 12:47:57 +08:00
1281 lines
44 KiB
C++
1281 lines
44 KiB
C++
#include <stdio.h>
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#include <math.h>
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#include <assert.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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#include "kalloc.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;
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uint32_t other_off;
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uint32_t cnt;
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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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#define an_key3(a) ((a).other_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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KRADIX_SORT_INIT(ha_an3, anchor1_t, an_key3, 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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#define oreg_id_lt(a, b) ((a).y_id < (b).y_id)
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KSORT_INIT(or_id, overlap_region, oreg_id_lt)
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typedef struct {
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int n;
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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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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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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_buf(void *km){HType *b = NULL; KCALLOC((km), b, 1); return b;}\
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HType *sf##_init(void){return (HType*)calloc(1, sizeof(HType));}\
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void sf##_free_buf(void *km, HType *ab, int is_z){if(ab){kfree(km, ab->seed); kfree(km, ab->a); kfree(km, ab->mz.a); if((is_z)){memset(ab, 0, sizeof(*ab));}}}\
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void sf##_destroy_buf(void *km, HType *ab){if(ab){kfree(km, ab->seed); kfree(km, ab->a); kfree(km, ab->mz.a); kfree(km, ab);}}\
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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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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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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, st_mt_t *sp)
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{
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uint32_t i, rlen;
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uint64_t k, l;
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uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
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uint32_t high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
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if(low_occ < 2) low_occ = 2;
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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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mz1_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, sp, asm_opt.mz_rewin, 0, 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->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->cnt = s->n;
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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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if(ab->a[k].cnt > low_occ && ab->a[k].cnt < high_occ){
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p->cnt = 1;
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}
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else if(ab->a[k].cnt <= low_occ){
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p->cnt = 2;
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}
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else{
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p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
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p->cnt = pow(p->cnt, 1.1);
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}
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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, NULL, bw_thres, keep_whole_chain, f_cigar, NULL);
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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 ha_get_new_ul_candidates(ha_abufl_t *ab, int64_t rid, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, 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, st_mt_t *sp, uint32_t high_occ, void *km)
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{
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uint32_t i;
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uint64_t k, l;
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if(high_occ < 1) high_occ = 1;
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// uint32_t high_occ = asm_opt.hom_cov >= 1?asm_opt.hom_cov:1;
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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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mz2_ha_sketch(rs, rl, mz_w, mz_k, 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, sp, asm_opt.mz_rewin, 0, km);
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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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KREALLOC(km, 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->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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KREALLOC(km, 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? rl - 1 - (z->pos + 1 - z->span) : z->pos;
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an->cnt = s->n;
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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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KREALLOC(km, 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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if(ab->a[k].cnt <= high_occ){
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p->cnt = 1;
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}
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else{
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p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
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p->cnt = pow(p->cnt, 1.1);
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}
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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, rl, NULL, uref, bw_thres, keep_whole_chain, f_cigar, km);
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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, rl);
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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, rl);
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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;
|
|
current_ID = candidates->list[i].readID;
|
|
current_stand = candidates->list[i].strand;
|
|
|
|
///reference read
|
|
(*f_cigar).x_id = readID;
|
|
(*f_cigar).x_pos_strand = current_stand;
|
|
///query read
|
|
(*f_cigar).y_id = current_ID;
|
|
///here the strand of query is always 0
|
|
(*f_cigar).y_pos_strand = 0;
|
|
|
|
sub_region_beg = i;
|
|
sub_region_end = i;
|
|
i++;
|
|
|
|
while (i < candidates->length
|
|
&&
|
|
current_ID == candidates->list[i].readID
|
|
&&
|
|
current_stand == candidates->list[i].strand)
|
|
{
|
|
sub_region_end = i;
|
|
i++;
|
|
}
|
|
|
|
if ((*f_cigar).x_id == (*f_cigar).y_id)
|
|
{
|
|
continue;
|
|
}
|
|
|
|
chain_len = chain_DP(candidates->list + sub_region_beg,
|
|
sub_region_end - sub_region_beg + 1, &(candidates->chainDP), f_cigar, band_width_threshold,
|
|
50, ua->a[(*f_cigar).x_id].len, ua->a[(*f_cigar).y_id].len, NULL);
|
|
|
|
|
|
// if ((*f_cigar).x_id != (*f_cigar).y_id)
|
|
if ((*f_cigar).x_id != (*f_cigar).y_id && chain_len > mz_occ*mz_rate)
|
|
{
|
|
append_utg_inexact_overlap_region_alloc(overlap_list, f_cigar, ua, add_beg_end, NULL);
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
void ha_get_inter_candidates(ha_abufl_t *ab, uint64_t id, char* r, uint64_t rlen, uint64_t rw, uint64_t rk, uint64_t is_hpc,
|
|
overlap_region_alloc *ol, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain,
|
|
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, st_mt_t *sp)
|
|
{
|
|
uint64_t i, k, l;
|
|
// prepare
|
|
clear_Candidates_list(cl);
|
|
clear_overlap_region_alloc(ol);
|
|
ab->mz.n = 0, ab->n_a = 0;
|
|
|
|
// get the list of anchors
|
|
mz2_ha_sketch(r, rlen, rw, rk, 0, is_hpc, &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct,
|
|
NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 1, NULL);
|
|
|
|
// minimizer of queried read
|
|
if (ab->mz.m > ab->old_mz_m) {
|
|
ab->old_mz_m = ab->mz.m;
|
|
REALLOC(ab->seed, ab->old_mz_m);
|
|
}
|
|
for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
|
|
int n;
|
|
ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
|
|
ab->seed[i].n = n;
|
|
ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x);
|
|
ab->n_a += n;
|
|
}
|
|
if (ab->n_a > ab->m_a) {
|
|
ab->m_a = ab->n_a;
|
|
kroundup64(ab->m_a);
|
|
REALLOC(ab->a, ab->m_a);
|
|
}
|
|
for (i = 0, k = 0; i < ab->mz.n; ++i) {
|
|
int j;
|
|
///z is one of the minimizer
|
|
ha_mzl_t *z = &ab->mz.a[i];
|
|
seedl_t *s = &ab->seed[i];
|
|
for (j = 0; j < s->n; ++j) {
|
|
const ha_idxposl_t *y = &s->a[j];
|
|
anchor1_t *an = &ab->a[k++];
|
|
uint8_t rev = z->rev == y->rev? 0 : 1;
|
|
an->other_off = y->pos;
|
|
an->self_off = rev? rlen - 1 - (z->pos + 1 - z->span) : z->pos;
|
|
an->cnt = s->n;
|
|
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
|
|
}
|
|
}
|
|
|
|
// sort anchors
|
|
radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
|
|
for (k = 1, l = 0; k <= ab->n_a; ++k) {
|
|
if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
|
|
if (k - l > 1)
|
|
radix_sort_ha_an2(ab->a + l, ab->a + k);
|
|
l = k;
|
|
}
|
|
}
|
|
|
|
|
|
// copy over to _cl_
|
|
if (ab->m_a >= (uint64_t)cl->size) {
|
|
cl->size = ab->m_a;
|
|
REALLOC(cl->list, cl->size);
|
|
}
|
|
for (k = 0; k < ab->n_a; ++k) {
|
|
k_mer_hit *p = &cl->list[k];
|
|
p->readID = ab->a[k].srt >> 33;
|
|
p->strand = ab->a[k].srt >> 32 & 1;
|
|
p->offset = ab->a[k].other_off;
|
|
p->self_offset = ab->a[k].self_off;
|
|
p->cnt = (ab->a[k].cnt == 1? 1 : 16);
|
|
}
|
|
cl->length = ab->n_a;
|
|
|
|
calculate_overlap_region_by_chaining(cl, ol, chain_idx, id, rlen, /**&R_INF**/NULL, NULL, bw_thres, keep_whole_chain, f_cigar, NULL);
|
|
|
|
#if 0
|
|
if (ol->length > 0) {
|
|
fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)ol->length, rlen);
|
|
for (int i = 0; i < (int)ol->length; ++i) {
|
|
overlap_region *r = &ol->list[i];
|
|
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],
|
|
(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));
|
|
}
|
|
}
|
|
#endif
|
|
|
|
if ((int)ol->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(ol->length, ol->list);
|
|
for (i = 0; i < (uint32_t)ol->length; ++i) {
|
|
const overlap_region *r = &ol->list[i];
|
|
w = ha_ov_type(r, rlen);
|
|
++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) {
|
|
// n[0] = n[1] = n[2] = n[3] = 0;
|
|
for (i = 0, k = 0; i < (uint32_t)ol->length; ++i) {
|
|
overlap_region *r = &ol->list[i];
|
|
w = ha_ov_type(r, rlen);
|
|
// ++n[w];
|
|
// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
|
|
if (r->shared_seed >= s[w]) {
|
|
if ((uint32_t)k != i) {
|
|
overlap_region t;
|
|
t = ol->list[k];
|
|
ol->list[k] = ol->list[i];
|
|
ol->list[i] = t;
|
|
}
|
|
++k;
|
|
}
|
|
}
|
|
ol->length = k;
|
|
}
|
|
}
|
|
|
|
///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
|
}
|
|
|
|
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,
|
|
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)
|
|
{
|
|
uint32_t i;
|
|
uint64_t k, l;
|
|
|
|
// prepare
|
|
clear_Candidates_list(cl);
|
|
clear_overlap_region_alloc(overlap_list);
|
|
ab->mz.n = 0, ab->n_a = 0;
|
|
|
|
// get the list of anchors
|
|
//should use the new version...
|
|
///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);
|
|
// minimizer of queried read
|
|
if (ab->mz.m > ab->old_mz_m) {
|
|
ab->old_mz_m = ab->mz.m;
|
|
REALLOC(ab->seed, ab->old_mz_m);
|
|
}
|
|
for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
|
|
int n;
|
|
ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &n);
|
|
ab->seed[i].n = n;
|
|
ab->n_a += n;
|
|
}
|
|
if (ab->n_a > ab->m_a) {
|
|
ab->m_a = ab->n_a;
|
|
kroundup64(ab->m_a);
|
|
REALLOC(ab->a, ab->m_a);
|
|
}
|
|
for (i = 0, k = 0; i < ab->mz.n; ++i) {
|
|
int j;
|
|
///z is one of the minimizer
|
|
ha_mz1_t *z = &ab->mz.a[i];
|
|
seed1_t *s = &ab->seed[i];
|
|
for (j = 0; j < s->n; ++j) {
|
|
const ha_idxpos_t *y = &s->a[j];
|
|
anchor1_t *an = &ab->a[k++];
|
|
uint8_t rev = z->rev == y->rev? 0 : 1;
|
|
an->other_off = y->pos;
|
|
an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos;
|
|
an->cnt = 1;
|
|
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
|
|
}
|
|
}
|
|
|
|
// sort anchors
|
|
radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
|
|
for (k = 1, l = 0; k <= ab->n_a; ++k) {
|
|
if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
|
|
if (k - l > 1)
|
|
radix_sort_ha_an2(ab->a + l, ab->a + k);
|
|
l = k;
|
|
}
|
|
}
|
|
|
|
|
|
// copy over to _cl_
|
|
if (ab->m_a >= (uint64_t)cl->size) {
|
|
cl->size = ab->m_a;
|
|
REALLOC(cl->list, cl->size);
|
|
}
|
|
for (k = 0; k < ab->n_a; ++k) {
|
|
k_mer_hit *p = &cl->list[k];
|
|
p->readID = ab->a[k].srt >> 33;
|
|
p->strand = ab->a[k].srt >> 32 & 1;
|
|
p->offset = ab->a[k].other_off;
|
|
p->self_offset = ab->a[k].self_off;
|
|
p->cnt = 1;
|
|
}
|
|
cl->length = ab->n_a;
|
|
|
|
calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
|
|
|
|
#if 0
|
|
if (overlap_list->length > 0) {
|
|
fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen);
|
|
for (int i = 0; i < (int)overlap_list->length; ++i) {
|
|
overlap_region *r = &overlap_list->list[i];
|
|
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],
|
|
(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));
|
|
}
|
|
}
|
|
#endif
|
|
|
|
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);
|
|
}
|
|
|
|
|
|
void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
|
|
{
|
|
uint64_t j = 0, inner_j = 0;
|
|
while (j < overlap_list->length && inner_j < paf->length)
|
|
{
|
|
if(overlap_list->list[j].y_id < paf->buffer[inner_j].tn)
|
|
{
|
|
j++;
|
|
}
|
|
else if(overlap_list->list[j].y_id > paf->buffer[inner_j].tn)
|
|
{
|
|
inner_j++;
|
|
}
|
|
else
|
|
{
|
|
if(overlap_list->list[j].y_pos_strand == paf->buffer[inner_j].rev)
|
|
{
|
|
overlap_list->list[j].is_match = 1;
|
|
}
|
|
j++;
|
|
inner_j++;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
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,
|
|
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,
|
|
kvec_t_u64_warp* dbg_ct, st_mt_t *sp)
|
|
{
|
|
extern void *ha_flt_tab;
|
|
extern ha_pt_t *ha_idx;
|
|
extern void *ha_flt_tab_hp;
|
|
extern ha_pt_t *ha_idx_hp;
|
|
|
|
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, sp);
|
|
|
|
if(ha_idx_hp)
|
|
{
|
|
uint32_t i, k, y_id, overlapLen, max_i;
|
|
int shared_seed;
|
|
overlap_region t;
|
|
overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
|
|
ma_hit_sort_tn(paf->buffer, paf->length);
|
|
ma_hit_sort_tn(rev_paf->buffer, rev_paf->length);
|
|
lable_matched_ovlp(overlap_list, paf);
|
|
lable_matched_ovlp(overlap_list, rev_paf);
|
|
|
|
for (i = 0, k = 0; i < overlap_list->length; ++i)
|
|
{
|
|
if(overlap_list->list[i].is_match == 1)
|
|
{
|
|
if(k != i)
|
|
{
|
|
t = overlap_list->list[k];
|
|
overlap_list->list[k] = overlap_list->list[i];
|
|
overlap_list->list[i] = t;
|
|
overlap_list->list[k].is_match = 0;
|
|
}
|
|
k++;
|
|
}
|
|
}
|
|
overlap_list->length = k;
|
|
|
|
|
|
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, sp);
|
|
|
|
if(overlap_list->length + overlap_list_hp->length > overlap_list->size)
|
|
{
|
|
overlap_list->list = (overlap_region*)realloc(overlap_list->list,
|
|
sizeof(overlap_region)*(overlap_list->length + overlap_list_hp->length));
|
|
memset(overlap_list->list + overlap_list->size, 0, sizeof(overlap_region)*
|
|
(overlap_list->length + overlap_list_hp->length - overlap_list->size));
|
|
overlap_list->size = overlap_list->length + overlap_list_hp->length;
|
|
}
|
|
|
|
for (i = 0, k = overlap_list->length; i < overlap_list_hp->length; i++, k++)
|
|
{
|
|
t = overlap_list->list[k];
|
|
overlap_list->list[k] = overlap_list_hp->list[i];
|
|
overlap_list_hp->list[i] = t;
|
|
}
|
|
overlap_list->length = k;
|
|
|
|
overlap_region_sort_y_id(overlap_list->list, overlap_list->length);
|
|
|
|
i = k = 0;
|
|
while (i < overlap_list->length)
|
|
{
|
|
y_id = overlap_list->list[i].y_id;
|
|
shared_seed = overlap_list->list[i].shared_seed;
|
|
overlapLen = overlap_list->list[i].overlapLen;
|
|
max_i = i;
|
|
i++;
|
|
while (i < overlap_list->length && overlap_list->list[i].y_id == y_id)
|
|
{
|
|
if((overlap_list->list[i].shared_seed > shared_seed) ||
|
|
((overlap_list->list[i].shared_seed == shared_seed) && (overlap_list->list[i].overlapLen <= overlapLen)))
|
|
{
|
|
y_id = overlap_list->list[i].y_id;
|
|
shared_seed = overlap_list->list[i].shared_seed;
|
|
overlapLen = overlap_list->list[i].overlapLen;
|
|
max_i = i;
|
|
}
|
|
i++;
|
|
}
|
|
|
|
if(k != max_i)
|
|
{
|
|
t = overlap_list->list[k];
|
|
overlap_list->list[k] = overlap_list->list[max_i];
|
|
overlap_list->list[max_i] = t;
|
|
}
|
|
k++;
|
|
}
|
|
|
|
overlap_list->length = k;
|
|
}
|
|
|
|
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
|
}
|
|
|
|
|
|
void ha_get_ul_candidates_interface(ha_abufl_t *ab, int64_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, overlap_region_alloc *overlap_list_hp, Candidates_list *cl, double bw_thres,
|
|
int max_n_chain, int keep_whole_chain, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* chain_idx, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t high_occ, void *km)
|
|
{
|
|
extern void *ha_flt_tab;
|
|
extern ha_pt_t *ha_idx;
|
|
|
|
ha_get_new_ul_candidates(ab, rid, rs, rl, mz_w, mz_k, uref, overlap_list, cl, bw_thres, max_n_chain, keep_whole_chain, k_flag, chain_idx, ha_flt_tab, ha_idx, f_cigar, dbg_ct, sp, high_occ, km);
|
|
if(km) {
|
|
ha_abufl_free_buf(km, ab, 1);
|
|
destory_Candidates_list_buf(km, cl, 1);
|
|
}
|
|
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
|
}
|
|
|
|
|
|
|
|
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list)
|
|
{
|
|
ks_introsort_or_xs(overlap_list->length, overlap_list->list);
|
|
}
|
|
|
|
|
|
void minimizers_gen(ha_abufl_t *ab, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag,
|
|
void *ha_flt_tab, ha_pt_t *ha_idx, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ)
|
|
{
|
|
// fprintf(stderr, "+[M::%s]\n", __func__);
|
|
uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0; int n, j; ha_mzl_t *z; seedl_t *s;
|
|
if(high_occ) {
|
|
max_cnt = (*high_occ);
|
|
if(max_cnt < 2) max_cnt = 2;
|
|
}
|
|
if(low_occ) {
|
|
min_cnt = (*low_occ);
|
|
if(min_cnt < 2) min_cnt = 2;
|
|
}
|
|
clear_Candidates_list(cl); ab->mz.n = 0, ab->n_a = 0;
|
|
|
|
// get the list of anchors
|
|
mz2_ha_sketch(rs, rl, mz_w, mz_k, 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, sp, asm_opt.mz_rewin, 0, NULL);
|
|
|
|
// minimizer of queried read
|
|
if (ab->mz.m > ab->old_mz_m) {
|
|
ab->old_mz_m = ab->mz.m;
|
|
REALLOC(ab->seed, ab->old_mz_m);
|
|
}
|
|
|
|
for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
|
|
ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
|
|
ab->seed[i].n = n;
|
|
ab->n_a += n;
|
|
}
|
|
|
|
if (ab->n_a > ab->m_a) {
|
|
ab->m_a = ab->n_a;
|
|
REALLOC(ab->a, ab->m_a);
|
|
}
|
|
|
|
for (i = 0, k = 0; i < ab->mz.n; ++i) {
|
|
///z is one of the minimizer
|
|
z = &ab->mz.a[i]; s = &ab->seed[i];
|
|
for (j = 0; j < s->n; ++j) {
|
|
const ha_idxposl_t *y = &s->a[j];
|
|
anchor1_t *an = &ab->a[k++];
|
|
uint8_t rev = z->rev == y->rev? 0 : 1;
|
|
an->other_off = y->pos;
|
|
an->self_off = rev? rl - 1 - (z->pos + 1 - z->span) : z->pos;
|
|
///an->cnt: cnt<<8|span
|
|
an->cnt = s->n; if(an->cnt > ((uint32_t)(0xffffffu))) an->cnt = 0xffffffu;
|
|
an->cnt <<= 8; an->cnt |= ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu)));
|
|
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
|
|
}
|
|
}
|
|
|
|
radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
|
|
for (k = 1, l = 0; k <= ab->n_a; ++k) {
|
|
if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
|
|
if (k - l > 1)
|
|
radix_sort_ha_an2(ab->a + l, ab->a + k);
|
|
l = k;
|
|
}
|
|
}
|
|
|
|
// copy over to _cl_
|
|
if (ab->m_a >= (uint64_t)cl->size) {
|
|
cl->size = ab->m_a;
|
|
REALLOC(cl->list, cl->size);
|
|
}
|
|
|
|
for (k = 0; k < ab->n_a; ++k) {
|
|
k_mer_hit *p = &cl->list[k];
|
|
p->readID = ab->a[k].srt >> 33;
|
|
p->strand = ab->a[k].srt >> 32 & 1;
|
|
p->offset = ab->a[k].other_off;
|
|
p->self_offset = ab->a[k].self_off;
|
|
if(((ab->a[k].cnt>>8) < max_cnt) && ((ab->a[k].cnt>>8) > min_cnt)){
|
|
p->cnt = 1;
|
|
} else if((ab->a[k].cnt>>8) <= min_cnt) {
|
|
p->cnt = 2;
|
|
} else{
|
|
p->cnt = 1 + (((ab->a[k].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
|
|
p->cnt = pow(p->cnt, 1.1);
|
|
}
|
|
if(p->cnt > ((uint32_t)(0xffffffu))) p->cnt = 0xffffffu;
|
|
p->cnt <<= 8; p->cnt |= (((uint32_t)(0xffu))&(ab->a[k].cnt));
|
|
}
|
|
cl->length = ab->n_a;
|
|
}
|
|
|
|
|
|
void minimizers_qgen(ha_abufl_t *ab, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag,
|
|
void *ha_flt_tab, ha_pt_t *ha_idx, All_reads* rdb, const ul_idx_t *udb, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ,
|
|
uint32_t *low_occ)
|
|
{
|
|
// fprintf(stderr, "+[M::%s]\n", __func__);
|
|
uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0; int n, j; ha_mzl_t *z; seedl_t *s;
|
|
if(high_occ) {
|
|
max_cnt = (*high_occ);
|
|
if(max_cnt < 2) max_cnt = 2;
|
|
}
|
|
if(low_occ) {
|
|
min_cnt = (*low_occ);
|
|
if(min_cnt < 2) min_cnt = 2;
|
|
}
|
|
clear_Candidates_list(cl); ab->mz.n = 0, ab->n_a = 0;
|
|
|
|
// get the list of anchors
|
|
mz2_ha_sketch(rs, rl, mz_w, mz_k, 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, sp, asm_opt.mz_rewin, 0, NULL);
|
|
|
|
// minimizer of queried read
|
|
if (ab->mz.m > ab->old_mz_m) {
|
|
ab->old_mz_m = ab->mz.m;
|
|
REALLOC(ab->seed, ab->old_mz_m);
|
|
}
|
|
|
|
for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
|
|
ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
|
|
ab->seed[i].n = n;
|
|
ab->n_a += n;
|
|
}
|
|
|
|
if (ab->n_a > ab->m_a) {
|
|
ab->m_a = ab->n_a;
|
|
REALLOC(ab->a, ab->m_a);
|
|
}
|
|
|
|
for (i = 0, k = 0; i < ab->mz.n; ++i) {
|
|
///z is one of the minimizer
|
|
z = &ab->mz.a[i]; s = &ab->seed[i];
|
|
for (j = 0; j < s->n; ++j) {
|
|
const ha_idxposl_t *y = &s->a[j];
|
|
anchor1_t *an = &ab->a[k++];
|
|
uint8_t rev = z->rev == y->rev? 0 : 1;
|
|
an->other_off = rev?((uint32_t)-1)-1-(y->pos+1-y->span):y->pos;
|
|
an->self_off = z->pos;
|
|
///an->cnt: cnt<<8|span
|
|
an->cnt = s->n; if(an->cnt > ((uint32_t)(0xffffffu))) an->cnt = 0xffffffu;
|
|
an->cnt <<= 8; an->cnt |= ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu)));
|
|
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->self_off;
|
|
}
|
|
}
|
|
|
|
// copy over to _cl_
|
|
if (ab->m_a >= (uint64_t)cl->size) {
|
|
cl->size = ab->m_a;
|
|
REALLOC(cl->list, cl->size);
|
|
}
|
|
|
|
k_mer_hit *p; uint64_t tid = (uint64_t)-1, tl = (uint64_t)-1;
|
|
radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
|
|
for (k = 1, l = 0; k <= ab->n_a; ++k) {
|
|
if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
|
|
if (k-l>1) radix_sort_ha_an3(ab->a+l, ab->a+k);
|
|
if((ab->a[l].srt>>33)!=tid) {
|
|
tid = ab->a[l].srt>>33;
|
|
tl = rdb?Get_READ_LENGTH((*rdb), tid):udb->ug->u.a[tid].len;
|
|
}
|
|
for (i = l; i < k; i++) {
|
|
p = &cl->list[i];
|
|
p->readID = ab->a[i].srt>>33;
|
|
p->strand = (ab->a[i].srt>>32)&1;
|
|
if(!(p->strand)) {
|
|
p->offset = ab->a[i].other_off;
|
|
} else {
|
|
p->offset = ((uint32_t)-1)-ab->a[i].other_off;
|
|
p->offset = tl-p->offset;
|
|
}
|
|
p->self_offset = ab->a[i].self_off;
|
|
if(((ab->a[i].cnt>>8) < max_cnt) && ((ab->a[i].cnt>>8) > min_cnt)){
|
|
p->cnt = 1;
|
|
} else if((ab->a[i].cnt>>8) <= min_cnt) {
|
|
p->cnt = 2;
|
|
} else{
|
|
p->cnt = 1 + (((ab->a[i].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
|
|
p->cnt = pow(p->cnt, 1.1);
|
|
}
|
|
if(p->cnt > ((uint32_t)(0xffffffu))) p->cnt = 0xffffffu;
|
|
p->cnt <<= 8; p->cnt |= (((uint32_t)(0xffu))&(ab->a[i].cnt));
|
|
}
|
|
l = k;
|
|
}
|
|
}
|
|
cl->length = ab->n_a;
|
|
}
|
|
|
|
void inline reverse_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t yl)
|
|
{
|
|
uint64_t z, han = a_n>>1; k_mer_hit *ai, *aj, ka;
|
|
for (z = 0; z < han; z++) {
|
|
ai = &(a[z]); aj = &(a[a_n-z-1]);
|
|
ka = (*ai); (*ai) = (*aj); (*aj) = ka;
|
|
|
|
ai->self_offset = xl-ai->self_offset-1;
|
|
ai->offset = yl-ai->offset-1;
|
|
|
|
aj->self_offset = xl-aj->self_offset-1;
|
|
aj->offset = yl-aj->offset-1;
|
|
}
|
|
if(a_n&1) {
|
|
a[z].self_offset = xl-a[z].self_offset-1;
|
|
a[z].offset = yl-a[z].offset-1;
|
|
}
|
|
}
|
|
|
|
|
|
void inline reset_k_mer_hit(k_mer_hit *a, uint64_t a_n, uint64_t xl, uint64_t yl, uint64_t rev, uint64_t *nid)
|
|
{
|
|
uint64_t z, han = a_n>>1; k_mer_hit *ai, *aj, ka;
|
|
if(rev) {
|
|
for (z = 0; z < han; z++) {
|
|
ai = &(a[z]); aj = &(a[a_n-z-1]);
|
|
ka = (*ai); (*ai) = (*aj); (*aj) = ka;
|
|
|
|
ai->self_offset = xl-ai->self_offset-1;
|
|
ai->offset = yl-ai->offset-1;
|
|
|
|
aj->self_offset = xl-aj->self_offset-1;
|
|
aj->offset = yl-aj->offset-1;
|
|
if(nid) ai->readID = aj->readID = (*nid);
|
|
}
|
|
if(a_n&1) {
|
|
a[z].self_offset = xl-a[z].self_offset-1;
|
|
a[z].offset = yl-a[z].offset-1;
|
|
if(nid) a[z].readID = (*nid);
|
|
}
|
|
} else if(nid) {
|
|
for (z = 0; z < a_n; z++) a[z].readID = (*nid);
|
|
}
|
|
}
|
|
|
|
void lchain_gen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
|
|
const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
|
|
int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
|
|
{
|
|
// fprintf(stderr, "+[M::%s]\n", __func__);
|
|
uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
|
|
clear_overlap_region_alloc(ol);
|
|
clear_fake_cigar(&(tf->f_cigar));
|
|
|
|
for (l = 0, k = 1, m = 0; k <= cn; k++) {
|
|
if((k == cn) || (cl->list[k].readID != cl->list[l].readID)
|
|
|| (cl->list[k].strand != cl->list[l].strand)) {
|
|
if(cl->list[l].readID != rid) {
|
|
tf->x_id = rid;
|
|
tf->x_pos_strand = cl->list[l].strand;
|
|
tf->y_id = cl->list[l].readID;
|
|
tf->y_pos_strand = 0;///always 0
|
|
// fprintf(stderr, "+[M::%s] l::%lu, k::%lu\n", __func__, l, k);
|
|
sm = lchain_dp(cl->list+l, k-l, cl->list+m, &(cl->chainDP), tf, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate,
|
|
rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, quick_check);
|
|
// assert(sm > 0);
|
|
if(ovlp_chain_gen(ol, tf, rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, apend_be, cl->list+m, sm)) {
|
|
r = &(ol->list[ol->length-1]); r->non_homopolymer_errors = m;
|
|
// if(r->y_pos_strand) {
|
|
// reverse_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
|
|
// }
|
|
reset_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len, r->y_pos_strand, &(ol->length));
|
|
if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
|
|
m += sm;
|
|
}
|
|
}
|
|
l = k;
|
|
}
|
|
}
|
|
cl->length = m;
|
|
|
|
|
|
k = ol->length;
|
|
if (ol->length > max_n_chain) {
|
|
int32_t w, n[4], s[4]; overlap_region t;
|
|
n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
|
|
ks_introsort_or_ss(ol->length, ol->list); ///srt = 1;
|
|
for (i = 0; i < ol->length; ++i) {
|
|
r = &(ol->list[i]);
|
|
w = ha_ov_type(r, rl);
|
|
++n[w];
|
|
if (((uint64_t)n[w]) == max_n_chain) s[w] = r->shared_seed;
|
|
}
|
|
if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
|
|
// n[0] = n[1] = n[2] = n[3] = 0;
|
|
for (i = 0, k = 0; i < ol->length; ++i) {
|
|
r = &(ol->list[i]);
|
|
w = ha_ov_type(r, rl);
|
|
// ++n[w];
|
|
// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) {
|
|
if (r->shared_seed >= s[w]) {
|
|
if (k != i) {
|
|
t = ol->list[k];
|
|
ol->list[k] = ol->list[i];
|
|
ol->list[i] = t;
|
|
}
|
|
++k;
|
|
}
|
|
}
|
|
ol->length = k;
|
|
}
|
|
}
|
|
/**
|
|
if(!gen_off) {
|
|
if(srt) ks_introsort_or_id(ol->length, ol->list);
|
|
uint64_t cln = cl->length;
|
|
for (i = k = m = 0; i < ol->length; ++i) {
|
|
r = &(ol->list[i]);
|
|
for (;(k<cln)&&((cl->list[k].readID!=r->y_id)||(cl->list[k].strand!=r->y_pos_strand)); k++);
|
|
// assert(k<cln);
|
|
for (cn = m; k < cln; k++, m++) {
|
|
if((cl->list[k].readID!=r->y_id)||(cl->list[k].strand!=r->y_pos_strand)) break;
|
|
if(m != k) cl->list[m] = cl->list[k];
|
|
}
|
|
// assert(m - cn > 0);
|
|
if(r->y_pos_strand) {
|
|
reverse_k_mer_hit(cl->list+cn, m-cn, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len);
|
|
}
|
|
// gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+cn, m-cn);
|
|
}
|
|
cl->length = m;
|
|
}
|
|
**/
|
|
|
|
ks_introsort_or_xs(ol->length, ol->list);
|
|
}
|
|
|
|
void lchain_qgen(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
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const ul_idx_t *udb, uint32_t apend_be, overlap_region* tf, uint64_t max_n_chain,
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int64_t max_skip, int64_t max_iter, int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check, uint32_t gen_off)
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{
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uint64_t i, k, l, m, sm, cn = cl->length; overlap_region *r; ///srt = 0
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clear_overlap_region_alloc(ol);
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clear_fake_cigar(&(tf->f_cigar));
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for (l = 0, k = 1, m = 0; k <= cn; k++) {
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if((k == cn) || (cl->list[k].readID != cl->list[l].readID)
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|| (cl->list[k].strand != cl->list[l].strand)) {
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if(cl->list[l].readID != rid) {
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tf->x_id = rid;
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tf->x_pos_strand = cl->list[l].strand;
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tf->y_id = cl->list[l].readID;
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tf->y_pos_strand = 0;///always 0
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// fprintf(stderr, "+[M::%s] l::%lu, k::%lu\n", __func__, l, k);
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sm = lchain_qdp(cl->list+l, k-l, cl->list+m, &(cl->chainDP), tf, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate,
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rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, quick_check);
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// assert(sm > 0);
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if(ovlp_chain_qgen(ol, tf, rl, rdb?Get_READ_LENGTH((*rdb), (*tf).y_id):udb->ug->u.a[(*tf).y_id].len, apend_be, cl->list+m, sm)) {
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r = &(ol->list[ol->length-1]); r->non_homopolymer_errors = m;
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// if(tf->y_id == 66 || tf->y_id == 66) {
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// fprintf(stderr, "\n[M::%s::] utg%.6dl(%c), i::%lu\n",
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// __func__, (int32_t)tf->y_id+1, "+-"[tf->x_pos_strand], m);
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// }
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// reset_k_mer_hit(cl->list+m, sm, rl, rdb?Get_READ_LENGTH((*rdb), r->y_id):udb->ug->u.a[r->y_id].len, r->y_pos_strand, &(ol->length));
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for (i = 0; i < sm; i++) {
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cl->list[m+i].readID = ol->length;
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// if(tf->y_id == 126) fprintf(stderr, "[M::%s::qoff->%u::toff->%u]\n", __func__, cl->list[m+i].self_offset, cl->list[m+i].offset);
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}
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if(gen_off) gen_fake_cigar(&(r->f_cigar), r, apend_be, cl->list+m, sm);
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m += sm;
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}
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}
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l = k;
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}
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}
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cl->length = m;
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// fprintf(stderr, "+[M::%s] cn::%lu, m::%lu, ol->length::%lu\n", __func__, cn, m, ol->length);
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// for (k = 0; k < ol->length; k++) {
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// fprintf(stderr, "---[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__,
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// (int32_t)ol->list[k].y_id+1, ol->list[k].x_pos_s, ol->list[k].x_pos_e+1,
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// ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
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// }
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k = ol->length;
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if (ol->length > max_n_chain) {
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int32_t w, n[4], s[4]; overlap_region t;
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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(ol->length, ol->list); ///srt = 1;
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for (i = 0; i < ol->length; ++i) {
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r = &(ol->list[i]);
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w = ha_ov_type(r, rl);
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++n[w];
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if (((uint64_t)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 < ol->length; ++i) {
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r = &(ol->list[i]);
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w = ha_ov_type(r, rl);
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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 (k != i) {
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t = ol->list[k];
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ol->list[k] = ol->list[i];
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ol->list[i] = t;
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}
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++k;
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}
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}
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ol->length = k;
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}
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}
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ks_introsort_or_xs(ol->length, ol->list);
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}
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void lchain_qgen_mcopy(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
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const ul_idx_t *udb, uint32_t apend_be, uint64_t max_n_chain, int64_t max_skip, int64_t max_iter,
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int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check,
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uint32_t gen_off)
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{
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// fprintf(stderr, "+[M::%s]\n", __func__);
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uint64_t i, k, l, m, cn = cl->length, yid; overlap_region *r; ///srt = 0
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clear_overlap_region_alloc(ol);
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for (l = 0, k = 1, m = 0; k <= cn; k++) {
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if((k == cn) || (cl->list[k].readID != cl->list[l].readID)) {
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if(cl->list[l].readID != rid) {
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yid = cl->list[l].readID;
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m += lchain_qdp_mcopy(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate,
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rid, rl, rdb?Get_READ_LENGTH((*rdb), yid):udb->ug->u.a[yid].len, quick_check, apend_be, gen_off);
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}
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l = k;
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}
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}
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cl->length = m;
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// for (k = 0; k < ol->length; k++) {
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// fprintf(stderr, "---[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), khit_off::%u\n", __func__,
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// (int32_t)ol->list[k].y_id+1, ol->list[k].x_pos_s, ol->list[k].x_pos_e+1,
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// ol->list[k].y_pos_s, ol->list[k].y_pos_e+1, ol->list[k].non_homopolymer_errors);
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// }
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k = ol->length;
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if (ol->length > max_n_chain) {
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int32_t w, n[4], s[4]; overlap_region t;
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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(ol->length, ol->list); ///srt = 1;
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for (i = 0; i < ol->length; ++i) {
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r = &(ol->list[i]);
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w = ha_ov_type(r, rl);
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++n[w];
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if (((uint64_t)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 < ol->length; ++i) {
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r = &(ol->list[i]);
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w = ha_ov_type(r, rl);
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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 (k != i) {
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t = ol->list[k];
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ol->list[k] = ol->list[i];
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ol->list[i] = t;
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}
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++k;
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}
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}
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ol->length = k;
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}
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}
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ks_introsort_or_xs(ol->length, ol->list);
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}
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void set_lchain_dp_op(uint32_t is_accurate, uint32_t mz_k, int64_t *max_skip, int64_t *max_iter, int64_t *max_dis, double *chn_pen_gap, double *chn_pen_skip, int64_t *quick_check)
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{
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double div, pen_gap, pen_skip, tmp;
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if(is_accurate) {
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(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.01; pen_gap = 0.5f; pen_skip = 0.0005f;
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} else {
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(*quick_check) = 0; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.1; pen_gap = 0.5f; pen_skip = 0.0005f;
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}
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tmp = expf(-div * (double)mz_k);///0.60049557881 -> HiFi; 0.18268352405 -> ont
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*chn_pen_gap = pen_gap * tmp;///0.300247789405 -> HiFi; 0.091341762025 -> ont
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///0.000300247789405 -> HiFi (>3330 will be negative);
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//0.000091341762025 -> ont (>10947 will be negative);
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*chn_pen_skip = pen_skip * tmp;
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}
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void ul_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, const ul_idx_t *uref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
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int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, overlap_region* f_cigar, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off)
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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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int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
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set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
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// minimizers_gen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, dbg_ct, sp, high_occ, low_occ);
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minimizers_qgen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, NULL, uref, dbg_ct, sp, high_occ, low_occ);
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// lchain_gen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
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// lchain_qgen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
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///no need to sort here, overlap_list has been sorted at lchain_gen
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lchain_qgen_mcopy(cl, overlap_list, rid, rl, NULL, uref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
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}
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