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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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Assembly.cpp
+9 -6
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@@ -13,7 +13,7 @@
#include "rcut.h"
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);
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);
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);
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
@@ -438,6 +438,7 @@ typedef struct {
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
ma_utg_v *ua;
st_mt_t sp;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
@@ -454,6 +455,7 @@ ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
kv_init(b->b_buf.a);
kv_init(b->r_buf.a);
kv_init(b->k_flag.a);
kv_init(b->sp);
b->ab = ha_abuf_init();
if (!b->is_final) {
init_Cigar_record(&b->cigar1);
@@ -478,6 +480,7 @@ void ha_ovec_destroy(ha_ovec_buf_t *b)
kv_destroy(b->b_buf.a);
kv_destroy(b->r_buf.a);
kv_destroy(b->k_flag.a);
kv_destroy(b->sp);
if (!b->is_final) {
destory_Cigar_record(&b->cigar1);
destory_Graph(&b->POA_Graph);
@@ -541,7 +544,7 @@ static void worker_ovec(void *data, long i, int tid)
int fully_cov, abnormal;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL);
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -599,7 +602,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
int fully_cov, abnormal, q_idx = k;
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist,
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), &(R_INF_FLAG.candidate_count[q_idx]));
0.02, asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), &(R_INF_FLAG.candidate_count[q_idx]), &(b->sp));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -625,7 +628,7 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
pthread_mutex_lock(&R_INF_FLAG.OutputMutex);
fprintf(R_INF_FLAG.fp, "\n>%.*s\n", (int)Get_NAME_LENGTH((R_INF), i), Get_NAME((R_INF), i));
fprintf(R_INF_FLAG.fp, "\n>%.*s, rid: %ld\n", (int)Get_NAME_LENGTH((R_INF), i), Get_NAME((R_INF), i), i);
fprintf(R_INF_FLAG.fp, "%d-th round, len: %lu, hom_cov: %d, max_n_chain: %d\n",
asm_opt.number_of_round, Get_READ_LENGTH(R_INF, i), asm_opt.hom_cov, asm_opt.max_n_chain);
@@ -1291,7 +1294,7 @@ static void worker_ov_final(void *data, long i, int tid)
//get_new_candidates(i, &g_read, &overlap_list, &array_list, &l, 0.001, 0);
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist, 0.001,
asm_opt.max_n_chain, 0, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL);
asm_opt.max_n_chain, 0, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
overlap_region_sort_y_id(b->olist.list, b->olist.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);
@@ -1357,7 +1360,7 @@ static void worker_ov_final_high_het(void *data, long i, int tid)
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
ha_get_candidates_interface(b->ab, i, &b->self_read, &b->olist, &b->olist_hp, &b->clist, HIGH_HET_ERROR_RATE,
asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL);
asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region), NULL, &(b->sp));
overlap_region_sort_y_id(b->olist.list, b->olist.length);
ma_hit_sort_tn(R_INF.paf[i].buffer, R_INF.paf[i].length);