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20a7dac82a0236bddfd56f5d2004a55b54d186fa
hifiasm/anchor.cpp
chhylp123 20a7dac82a backup for minimizer
2022-09-28 11:16:09 -04:00

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#include <stdio.h>
#include <math.h>
#include <assert.h>
#include "htab.h"
#include "ksort.h"
#include "Hash_Table.h"
#include "kalloc.h"
#define HA_KMER_GOOD_RATIO 0.333
typedef struct { // this struct is not strictly necessary; we can use k_mer_pos instead, with modifications
uint64_t srt;
uint32_t self_off;
uint32_t other_off;
uint32_t cnt;
} anchor1_t;
#define an_key1(a) ((a).srt)
#define an_key2(a) ((a).self_off)
KRADIX_SORT_INIT(ha_an1, anchor1_t, an_key1, 8)
KRADIX_SORT_INIT(ha_an2, anchor1_t, an_key2, 4)
#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))
KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
#define oreg_ss_lt(a, b) ((a).shared_seed > (b).shared_seed) // in the decending order
KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)
#define oreg_id_lt(a, b) ((a).y_id < (b).y_id)
KSORT_INIT(or_id, overlap_region, oreg_id_lt)
typedef struct {
int n;
const ha_idxpos_t *a;
} seed1_t;
typedef struct {
int n, cnt;
const ha_idxposl_t *a;
} seedl_t;
struct ha_abuf_s {
uint64_t n_a, m_a;///number of anchors (seed positions)
uint32_t old_mz_m;///number of seeds
ha_mz1_v mz;
seed1_t *seed;
anchor1_t *a;
};
struct ha_abufl_s {
uint64_t n_a, m_a;///number of anchors (seed positions)
uint32_t old_mz_m;///number of seeds
ha_mzl_v mz;
seedl_t *seed;
anchor1_t *a;
};
#define HA_ABUF_INIT(HType, MZType, SDType, sf) \
HType *sf##_init_buf(void *km){HType *b = NULL; KCALLOC((km), b, 1); return b;}\
HType *sf##_init(void){return (HType*)calloc(1, sizeof(HType));}\
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));}}}\
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);}}\
void sf##_destroy(HType *ab){if(ab){free(ab->seed); free(ab->a); free(ab->mz.a); free(ab);}}\
uint64_t sf##_mem(const HType *ab){\
return ab->m_a * sizeof(anchor1_t) + ab->mz.m * (sizeof(MZType) + sizeof(SDType)) + sizeof(HType);\
}
HA_ABUF_INIT(ha_abuf_s, ha_mz1_t, seed1_t, ha_abuf)
HA_ABUF_INIT(ha_abufl_s, ha_mzl_t, seedl_t, ha_abufl)
int ha_ov_type(const overlap_region *r, uint32_t len)
{
if (r->x_pos_s == 0 && r->x_pos_e == len - 1) return 2; // contained in a longer read
else if (r->x_pos_s > 0 && r->x_pos_e < len - 1) return 3; // containing a shorter read
else return r->x_pos_s == 0? 0 : 1;
}
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,
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 i, rlen;
uint64_t k, l;
uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
uint32_t high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
if(low_occ < 2) low_occ = 2;
// prepare
clear_Candidates_list(cl);
clear_overlap_region_alloc(overlap_list);
recover_UC_Read(ucr, &R_INF, rid);
ab->mz.n = 0, ab->n_a = 0;
rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors
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);
// 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? ucr->length - 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;
if(ab->a[k].cnt > low_occ && ab->a[k].cnt < high_occ){
p->cnt = 1;
}
else if(ab->a[k].cnt <= low_occ){
p->cnt = 2;
}
else{
p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
p->cnt = pow(p->cnt, 1.1);
}
}
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, ucr->length, &R_INF, NULL, bw_thres, keep_whole_chain, f_cigar, NULL);
#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, 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)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->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 = 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 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,
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)
{
uint32_t i;
uint64_t k, l;
if(high_occ < 1) high_occ = 1;
// uint32_t high_occ = asm_opt.hom_cov >= 1?asm_opt.hom_cov:1;
// prepare
clear_Candidates_list(cl);
clear_overlap_region_alloc(overlap_list);
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, km);
// minimizer of queried read
if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m;
KREALLOC(km, 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->n_a += n;
}
if (ab->n_a > ab->m_a) {
ab->m_a = ab->n_a;
KREALLOC(km, 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? rl - 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;
KREALLOC(km, 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 <= high_occ){
p->cnt = 1;
}
else{
p->cnt = 1 + ((ab->a[k].cnt + (high_occ<<1) - 1)/(high_occ<<1));
p->cnt = pow(p->cnt, 1.1);
}
}
cl->length = ab->n_a;
calculate_overlap_region_by_chaining(cl, overlap_list, chain_idx, rid, rl, NULL, uref, bw_thres, keep_whole_chain, f_cigar, km);
#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, rl);
++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)overlap_list->length; ++i) {
overlap_region *r = &overlap_list->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 ((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 calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list, kvec_t_u64_warp* chain_idx,
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)
{
long long i = 0;
uint64_t current_ID;
uint64_t current_stand;
if (candidates->length == 0)
{
return;
}
long long sub_region_beg;
long long sub_region_end;
long long chain_len;
clear_fake_cigar(&((*f_cigar).f_cigar));
i = 0;
while (i < candidates->length)
{
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 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 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)
{
double div, pen_gap, pen_skip, tmp;
if(is_accurate) {
(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.01; pen_gap = 0.5f; pen_skip = 0.0005f;
} else {
(*quick_check) = 1; (*max_skip) = 25; (*max_iter) = 5000; (*max_dis) = 5000; div = 0.1; pen_gap = 0.5f; pen_skip = 0.0005f;
}
tmp = expf(-div * (double)mz_k);///0.60049557881 -> HiFi; 0.18268352405 -> ont
*chn_pen_gap = pen_gap * tmp;///0.300247789405 -> HiFi; 0.091341762025 -> ont
///0.000300247789405 -> HiFi (>3330 will be negative);
//0.000091341762025 -> ont (>10947 will be negative);
*chn_pen_skip = pen_skip * tmp;
}
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,
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)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
int64_t max_skip, max_iter, max_dis, quick_check; double chn_pen_gap, chn_pen_skip;
set_lchain_dp_op(is_accurate, mz_k, &max_skip, &max_iter, &max_dis, &chn_pen_gap, &chn_pen_skip, &quick_check);
minimizers_gen(ab, rs, rl, mz_w, mz_k, cl, k_flag, ha_flt_tab, ha_idx, dbg_ct, sp, high_occ, low_occ);
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);
///no need to sort here, overlap_list has been sorted at lchain_gen
}
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