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better seeding

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chhylp123
2021-08-22 09:53:34 -04:00
parent bfff640a82
commit 37b07e4d33
15 changed files with 637 additions and 406 deletions
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40
anchor.cpp
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@@ -1,4 +1,5 @@
#include <stdio.h>
#include <math.h>
#include "htab.h"
#include "ksort.h"
#include "Hash_Table.h"
@@ -7,8 +8,9 @@
typedef struct { // this struct is not strictly necessary; we can use k_mer_pos instead, with modifications
uint64_t srt;
uint32_t self_off:31, good:1;
uint32_t self_off;
uint32_t other_off;
uint32_t cnt;
} anchor1_t;
#define an_key1(a) ((a).srt)
@@ -23,7 +25,7 @@ KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
KSORT_INIT(or_ss, overlap_region, oreg_ss_lt)
typedef struct {
int n, good;
int n;
const ha_idxpos_t *a;
} seed1_t;
@@ -58,12 +60,13 @@ int ha_ov_type(const overlap_region *r, uint32_t len)
}
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)
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;
double low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
double high_occ = asm_opt.hom_cov * (2.0 - HA_KMER_GOOD_RATIO);
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);
@@ -73,7 +76,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
rlen = Get_READ_LENGTH(R_INF, rid); // read length
// get the list of anchors
ha_sketch(ucr->seq, ucr->length, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, NULL);
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);
// minimizer of queried read
if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m;
@@ -83,7 +86,6 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
int n;
ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &n);
ab->seed[i].n = n;
ab->seed[i].good = (n > low_occ && n < high_occ);
ab->n_a += n;
}
if (ab->n_a > ab->m_a) {
@@ -102,7 +104,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
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->good = s->good;
an->cnt = s->n;
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
}
}
@@ -129,7 +131,16 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
p->strand = ab->a[k].srt >> 32 & 1;
p->offset = ab->a[k].other_off;
p->self_offset = ab->a[k].self_off;
p->good = ab->a[k].good;
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;
@@ -269,7 +280,6 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
int n;
ab->seed[i].a = ha_pt_get(ha_idx, ab->mz.a[i].x, &n);
ab->seed[i].n = n;
ab->seed[i].good = 0;
ab->n_a += n;
}
if (ab->n_a > ab->m_a) {
@@ -288,7 +298,7 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
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->good = s->good;
an->cnt = 1;
an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
}
}
@@ -315,7 +325,7 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
p->strand = ab->a[k].srt >> 32 & 1;
p->offset = ab->a[k].other_off;
p->self_offset = ab->a[k].self_off;
p->good = ab->a[k].good;
p->cnt = 1;
}
cl->length = ab->n_a;
@@ -391,14 +401,14 @@ void lable_matched_ovlp(overlap_region_alloc* overlap_list, ma_hit_t_alloc* paf)
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)
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);
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)
{
@@ -428,7 +438,7 @@ void ha_get_candidates_interface(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overl
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);
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)
{