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freeze-r304

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chhylp123
2020-08-23 23:34:36 -04:00
parent 03cf0d475c
commit 724990cbe7
7 changed files with 235 additions and 74 deletions
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Assembly.cpp
+17 -14
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@@ -12,7 +12,7 @@
#include "kthread.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, ma_hit_t_alloc* paf, ma_hit_t_alloc* rev_paf);
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);
void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
All_reads R_INF;
@@ -457,6 +457,7 @@ typedef struct {
kvec_t_u32_warp b_buf;
kvec_t_u64_warp r_buf;
kvec_t_u8_warp k_flag;
overlap_region tmp_region;
} ha_ovec_buf_t;
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
@@ -469,6 +470,7 @@ ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov)
init_Candidates_list(&b->clist);
init_overlap_region_alloc(&b->olist);
init_overlap_region_alloc(&b->olist_hp);
init_fake_cigar(&(b->tmp_region.f_cigar));
kv_init(b->b_buf.a);
kv_init(b->r_buf.a);
kv_init(b->k_flag.a);
@@ -492,6 +494,7 @@ void ha_ovec_destroy(ha_ovec_buf_t *b)
destory_overlap_region_alloc(&b->olist);
destory_overlap_region_alloc(&b->olist_hp);
ha_abuf_destroy(b->ab);
destory_fake_cigar(&(b->tmp_region.f_cigar));
kv_destroy(b->b_buf.a);
kv_destroy(b->r_buf.a);
kv_destroy(b->k_flag.a);
@@ -558,7 +561,7 @@ 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), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
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));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -581,10 +584,10 @@ static void worker_ovec(void *data, long i, int tid)
R_INF.paf[i].is_abnormal = abnormal;
R_INF.trio_flag[i] = AMBIGU;
if(ha_idx_hp == NULL)
{
R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &b->b_buf, &b->r_buf, &(b->k_flag), RESEED_HP_RATE, NULL);
}
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), NULL);
// }
if (R_INF.trio_flag[i] != AMBIGU || b->save_ov) {
int is_rev = (asm_opt.number_of_round % 2 == 0);
@@ -615,7 +618,7 @@ static void worker_ovec_related_reads(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), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
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));
clear_Cigar_record(&b->cigar1);
clear_Round2_alignment(&b->round2);
@@ -679,10 +682,10 @@ static void worker_ovec_related_reads(void *data, long i, int tid)
}
R_INF.trio_flag[i] = AMBIGU;
if(ha_idx_hp == NULL)
{
R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &b->b_buf, &b->r_buf, &(b->k_flag), RESEED_HP_RATE, R_INF_FLAG.fp);
}
// if(ha_idx_hp == NULL)
// {
// R_INF.trio_flag[i] += collect_hp_regions(&b->olist, &R_INF, &(b->k_flag), RESEED_HP_RATE, Get_READ_LENGTH(R_INF, i), R_INF_FLAG.fp);
// }
fprintf(R_INF_FLAG.fp, "R_INF.trio_flag[%ld]: %u\n", i, R_INF.trio_flag[i]);
@@ -891,7 +894,7 @@ void ha_overlap_and_correct(int round)
free(e[i].second_round_read);
}
free(e);
debug_print_pob_regions();
///debug_print_pob_regions();
}
@@ -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), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
asm_opt.max_n_chain, 0, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
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), &(R_INF.paf[i]), &(R_INF.reverse_paf[i]));
asm_opt.max_n_chain, 1, &(b->k_flag), &b->r_buf, &(R_INF.paf[i]), &(R_INF.reverse_paf[i]), &(b->tmp_region));
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);