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chhylp123
2021-09-16 17:16:30 -04:00
parent ab80851b94
commit ed814abf35
2 changed files with 180 additions and 137 deletions
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anchor.cpp
+107 -110
View File
@@ -265,130 +265,127 @@ void calculate_ug_chaining(Candidates_list* candidates, overlap_region_alloc* ov
} }
} }
/**
void ha_get_inter_candidates(ha_abufl_t *ab, int64_t uid, ma_utg_v *ua, overlap_region_alloc *ovlp,
Candidates_list *cl, double bw_thres, int max_n_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,
double chain_match_rate, uint32_t uk, uint32_t uw, uint32_t is_hpc, uint32_t h_occ)
{
uint32_t i, rlen; 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,
uint64_t k, l; overlap_region_alloc *ol, Candidates_list *cl, double bw_thres, int max_n_chain, int keep_whole_chain,
ma_utg_t *u = &(ua->a[uid]); 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 // prepare
clear_Candidates_list(cl); clear_Candidates_list(cl);
clear_overlap_region_alloc(ovlp); clear_overlap_region_alloc(ol);
ab->mz.n = 0, ab->n_a = 0; ab->mz.n = 0, ab->n_a = 0;
mz2_ha_sketch(u->s, u->len, uw, uk, uid, is_hpc, &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, // get the list of anchors
NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 1); 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);
// minimizer of queried read // minimizer of queried read
if (ab->mz.m > ab->old_mz_m) { if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m; ab->old_mz_m = ab->mz.m;
REALLOC(ab->seed, ab->old_mz_m); REALLOC(ab->seed, ab->old_mz_m);
} }
for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) { for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
int n; int n;
ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n); ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
ab->seed[i].n = n; ab->seed[i].n = n;
ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x); ab->seed[i].cnt = ha_ft_cnt(ha_flt_tab, ab->mz.a[i].x);
ab->n_a += n; ab->n_a += n;
} }
if (ab->n_a > ab->m_a) { if (ab->n_a > ab->m_a) {
ab->m_a = ab->n_a; ab->m_a = ab->n_a;
kroundup64(ab->m_a); kroundup64(ab->m_a);
REALLOC(ab->a, ab->m_a); REALLOC(ab->a, ab->m_a);
} }
for (i = 0, k = 0; i < ab->mz.n; ++i) { for (i = 0, k = 0; i < ab->mz.n; ++i) {
int j; int j;
///z is one of the minimizer ///z is one of the minimizer
ha_mzl_t *z = &ab->mz.a[i]; ha_mzl_t *z = &ab->mz.a[i];
seedl_t *s = &ab->seed[i]; seedl_t *s = &ab->seed[i];
for (j = 0; j < s->n; ++j) { for (j = 0; j < s->n; ++j) {
const ha_idxposl_t *y = &s->a[j]; const ha_idxposl_t *y = &s->a[j];
anchor1_t *an = &ab->a[k++]; anchor1_t *an = &ab->a[k++];
uint8_t rev = z->rev == y->rev? 0 : 1; uint8_t rev = z->rev == y->rev? 0 : 1;
an->other_off = y->pos; an->other_off = y->pos;
an->self_off = rev? u->len - 1 - (z->pos + 1 - z->span) : z->pos; an->self_off = rev? rlen - 1 - (z->pos + 1 - z->span) : z->pos;
an->cnt = s->cnt; an->cnt = s->n;
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off; an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
} }
} }
// sort anchors // sort anchors
radix_sort_ha_an1(ab->a, ab->a + ab->n_a); radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
for (k = 1, l = 0; k <= ab->n_a; ++k) { 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 == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
if (k - l > 1) if (k - l > 1)
radix_sort_ha_an2(ab->a + l, ab->a + k); radix_sort_ha_an2(ab->a + l, ab->a + k);
l = k; l = k;
} }
} }
// copy over to _cl_ // copy over to _cl_
if (ab->m_a >= (uint64_t)cl->size) { if (ab->m_a >= (uint64_t)cl->size) {
cl->size = ab->m_a; cl->size = ab->m_a;
REALLOC(cl->list, cl->size); REALLOC(cl->list, cl->size);
} }
for (k = 0; k < ab->n_a; ++k) { for (k = 0; k < ab->n_a; ++k) {
k_mer_hit *p = &cl->list[k]; k_mer_hit *p = &cl->list[k];
p->readID = ab->a[k].srt >> 33; p->readID = ab->a[k].srt >> 33;
p->strand = ab->a[k].srt >> 32 & 1; p->strand = ab->a[k].srt >> 32 & 1;
p->offset = ab->a[k].other_off; p->offset = ab->a[k].other_off;
p->self_offset = ab->a[k].self_off; p->self_offset = ab->a[k].self_off;
p->cnt = (ab->a[k].cnt == 1? 1 : 16); p->cnt = (ab->a[k].cnt == 1? 1 : 16);
} }
cl->length = ab->n_a; cl->length = ab->n_a;
// calculate_overlap_region_by_chaining(cl, ovlp, chain_idx, rid, ucr->length, &R_INF, bw_thres, keep_whole_chain, f_cigar);
// calculate_ug_chaining(cl, overlap_list, chain_idx, rid, ua, bw_thres, keep_whole_chain, f_cigar, ab->mz.n, chain_match_rate);
calculate_overlap_region_by_chaining(cl, ol, chain_idx, id, rlen, &R_INF, bw_thres, keep_whole_chain, f_cigar);
#if 0 #if 0
if (overlap_list->length > 0) { if (ol->length > 0) {
fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)overlap_list->length, rlen); fprintf(stderr, "B\t%ld\t%ld\t%d\n", (long)rid, (long)ol->length, rlen);
for (int i = 0; i < (int)overlap_list->length; ++i) { for (int i = 0; i < (int)ol->length; ++i) {
overlap_region *r = &overlap_list->list[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], 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)); (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 #endif
if ((int)ovlp->length > max_n_chain) { if ((int)ol->length > max_n_chain) {
int32_t w, n[4], s[4]; 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; n[0] = n[1] = n[2] = n[3] = 0, s[0] = s[1] = s[2] = s[3] = 0;
ks_introsort_or_ss(ovlp->length, ovlp->list); ks_introsort_or_ss(ol->length, ol->list);
for (i = 0; i < (uint32_t)ovlp->length; ++i) { for (i = 0; i < (uint32_t)ol->length; ++i) {
const overlap_region *r = &ovlp->list[i]; const overlap_region *r = &ol->list[i];
w = ha_ov_type(r, rlen); w = ha_ov_type(r, rlen);
++n[w]; ++n[w];
if ((int)n[w] == max_n_chain) s[w] = r->shared_seed; 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) { if (s[0] > 0 || s[1] > 0 || s[2] > 0 || s[3] > 0) {
// n[0] = n[1] = n[2] = n[3] = 0; // n[0] = n[1] = n[2] = n[3] = 0;
for (i = 0, k = 0; i < (uint32_t)ovlp->length; ++i) { for (i = 0, k = 0; i < (uint32_t)ol->length; ++i) {
overlap_region *r = &ovlp->list[i]; overlap_region *r = &ol->list[i];
w = ha_ov_type(r, rlen); w = ha_ov_type(r, rlen);
// ++n[w]; // ++n[w];
// if (((int)n[w] <= max_n_chain) || (r->shared_seed >= s[w] && s[w] >= (asm_opt.k_mer_length<<1))) { // 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 (r->shared_seed >= s[w]) {
if ((uint32_t)k != i) { if ((uint32_t)k != i) {
overlap_region t; overlap_region t;
t = ovlp->list[k]; t = ol->list[k];
ovlp->list[k] = ovlp->list[i]; ol->list[k] = ol->list[i];
ovlp->list[i] = t; ol->list[i] = t;
} }
++k; ++k;
} }
} }
ovlp->length = k; ol->length = k;
} }
} }
///ks_introsort_or_xs(overlap_list->length, overlap_list->list);
///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, 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) 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)
inter.cpp
+72 -26
View File
@@ -8,12 +8,20 @@
#include "Overlaps.h" #include "Overlaps.h"
#include "CommandLines.h" #include "CommandLines.h"
#include "htab.h" #include "htab.h"
#include "Hash_Table.h"
KSEQ_INIT(gzFile, gzread) KSEQ_INIT(gzFile, gzread)
typedef struct { typedef struct {
int w, k, bw, max_gap, is_HPC, hap_n; int w, k, bw, max_gap, is_HPC, hap_n;
} mg_idxopt_t; } mg_idxopt_t;
typedef struct {
ha_abufl_t *abl;
st_mt_t sp;
Candidates_list clist;
overlap_region_alloc olist;
} ma_ov_buf_t;
typedef struct { // global data structure for kt_pipeline() typedef struct { // global data structure for kt_pipeline()
const void *ha_flt_tab; const void *ha_flt_tab;
const ha_pt_t *ha_idx; const ha_pt_t *ha_idx;
@@ -25,6 +33,39 @@ typedef struct { // global data structure for kt_pipeline()
uint64_t total_pair; uint64_t total_pair;
} uldat_t; } uldat_t;
typedef struct { // data structure for each step in kt_pipeline()
const void *ha_flt_tab;
const ha_pt_t *ha_idx;
int n, m, sum_len;
uint64_t *len, id;
char **seq;
ma_ov_buf_t **mo;
} utepdat_t;
ma_ov_buf_t **init_ma_ov_buf_t_arr(uint64_t n)
{
uint64_t i;
ma_ov_buf_t **p = NULL; CALLOC(p, 1); CALLOC(*p, n);
for (i = 0; i < n; i++){
kv_init((*p)[i].sp); (*p)[i].abl = ha_abufl_init();
init_Candidates_list(&((*p)[i].clist));
init_overlap_region_alloc(&((*p)[i].olist));
}
return p;
}
void destory_ma_ov_buf_t_arr(ma_ov_buf_t ***p, uint64_t n)
{
uint64_t i;
for (i = 0; i < n; i++){
kv_destroy((**p)[i].sp); ha_abufl_destroy((**p)[i].abl);
destory_Candidates_list(&((**p)[i].clist));
destory_overlap_region_alloc(&((**p)[i].olist));
}
free((**p)); free((*p));
}
void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n) void init_mg_opt(mg_idxopt_t *opt, int is_HPC, int k, int w, int hap_n)
{ {
opt->k = k; opt->k = k;
@@ -50,33 +91,39 @@ void uidx_destory()
ha_pt_destroy(ha_idx); ha_pt_destroy(ha_idx);
} }
static void worker_for_ul_alignment(void *data, long i, int tid) // callback for kt_for()
{
utepdat_t *s = (utepdat_t*)data;
ma_ov_buf_t *b = s->mo[tid];
uint64_t len = s->len[i];
char *r = s->seq[i];
}
static void *worker_ul_pipeline(void *data, int step, void *in) // callback for kt_pipeline() static void *worker_ul_pipeline(void *data, int step, void *in) // callback for kt_pipeline()
{ {
/**
uldat_t *p = (uldat_t*)data; uldat_t *p = (uldat_t*)data;
///uint64_t total_base = 0, total_pair = 0; ///uint64_t total_base = 0, total_pair = 0;
if (step == 0) { // step 1: read a block of sequences if (step == 0) { // step 1: read a block of sequences
int ret1, ret2; int ret;
uint64_t l1, l2; uint64_t l;
stepdat_t *s; utepdat_t *s;
CALLOC(s, 1); CALLOC(s, 1);
s->idx = p->idx; s->id = p->total_pair; s->t_ch = p->t_ch; s->ha_flt_tab = p->ha_flt_tab; s->ha_idx = p->ha_idx; s->id = p->total_pair;
while (((ret1 = kseq_read(p->ks1)) >= 0)&&((ret2 = kseq_read(p->ks2)) >= 0)) while ((ret = kseq_read(p->ks)) >= 0)
{ {
if (p->ks1->seq.l < p->idx->k || p->ks2->seq.l < p->idx->k) continue; if (p->ks->seq.l < (uint64_t)p->opt->k) continue;
if (s->n == s->m) { if (s->n == s->m) {
s->m = s->m < 16? 16 : s->m + (s->n>>1); s->m = s->m < 16? 16 : s->m + (s->n>>1);
REALLOC(s->len, s->m); REALLOC(s->len, s->m);
REALLOC(s->seq, s->m); REALLOC(s->seq, s->m);
} }
l = p->ks->seq.l;
l1 = p->ks1->seq.l; l2 = p->ks2->seq.l; MALLOC(s->seq[s->n], l);
MALLOC(s->seq[s->n], l1+l2); s->sum_len += l;
s->sum_len += l1+l2; memcpy(s->seq[s->n], p->ks->seq.s, l);
memcpy(s->seq[s->n], p->ks1->seq.s, l1); s->len[s->n++] = l;
memcpy(s->seq[s->n]+l1, p->ks2->seq.s, l2);
s->len[s->n++] = (uint64_t)(l1<<32)|(uint64_t)l2;
if (s->sum_len >= p->chunk_size) break; if (s->sum_len >= p->chunk_size) break;
} }
p->total_pair += s->n; p->total_pair += s->n;
@@ -84,25 +131,24 @@ static void *worker_ul_pipeline(void *data, int step, void *in) // callback for
else return s; else return s;
} }
else if (step == 1) { // step 2: alignment else if (step == 1) { // step 2: alignment
stepdat_t *s = (stepdat_t*)in; utepdat_t *s = (utepdat_t*)in;
CALLOC(s->pos_buf, p->n_thread); s->mo = init_ma_ov_buf_t_arr(p->n_thread);
/**
CALLOC(s->pos, s->n); CALLOC(s->pos, s->n);
**/
int i; int i;
kt_for(p->n_thread, worker_for_alignment, s, s->n); kt_for(p->n_thread, worker_for_ul_alignment, s, s->n);
for (i = 0; i < s->n; ++i) { for (i = 0; i < s->n; ++i) {
free(s->seq[i]); free(s->seq[i]);
p->total_base += (s->len[i]>>32) + (uint32_t)s->len[i]; p->total_base += s->len[i];
} }
free(s->seq); free(s->len); free(s->seq); free(s->len);
for (i = 0; i < (int)p->n_thread; ++i) { destory_ma_ov_buf_t_arr(&(s->mo), p->n_thread);
free(s->pos_buf[i].a.a);
}
free(s->pos_buf);
return s; return s;
} }
else if (step == 2) { // step 3: dump else if (step == 2) { // step 3: dump
stepdat_t *s = (stepdat_t*)in; utepdat_t *s = (utepdat_t*)in;
/**
int i; int i;
for (i = 0; i < s->n; ++i) { for (i = 0; i < s->n; ++i) {
// if(s->pos[i].a == NULL) continue; // if(s->pos[i].a == NULL) continue;
@@ -111,9 +157,9 @@ static void *worker_ul_pipeline(void *data, int step, void *in) // callback for
kv_push(pe_hit, p->hits.a, s->pos[i]); kv_push(pe_hit, p->hits.a, s->pos[i]);
} }
free(s->pos); free(s->pos);
**/
free(s); free(s);
} }
**/
return 0; return 0;
} }