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integration/print het sites

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chhylp123
2022-01-17 18:29:48 -05:00
parent 7af0d85258
commit 0ce5a7ba5b
18 changed files with 2884 additions and 385 deletions
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65
Assembly.cpp
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@@ -11,6 +11,7 @@
#include "htab.h"
#include "kthread.h"
#include "rcut.h"
#include "kalloc.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, st_mt_t *sp);
@@ -21,6 +22,7 @@ void ha_sort_list_by_anchor(overlap_region_alloc *overlap_list);
All_reads R_INF;
Debug_reads R_INF_FLAG;
all_ul_t UL_INF;
uint32_t *het_cnt = NULL;
void get_corrected_read_from_cigar(Cigar_record* cigar, char* pre_read, int pre_length, char* new_read, int* new_length)
{
@@ -418,6 +420,36 @@ long long push_final_overlaps_increment(ma_hit_t_alloc* paf, ma_hit_t_alloc* rev
return available_overlaps;
}
ha_ovec_buf_t *ha_ovec_buf_init(void *km, int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;
KCALLOC(km, b, 1);
b->is_final = !!is_final, b->save_ov = !!save_ov;
init_UC_Read(&b->self_read);//set 0
init_UC_Read(&b->ovlp_read);//set 0
init_Candidates_list(&b->clist);//set 0
memset(&b->olist, 0, sizeof(overlap_region_alloc));
memset(&b->olist_hp, 0, sizeof(overlap_region_alloc));
// init_overlap_region_alloc(&b->olist);
// init_overlap_region_alloc(&b->olist_hp);
init_fake_cigar(&(b->tmp_region.f_cigar));//set 0
kv_init(b->b_buf.a);//set 0
kv_init(b->r_buf.a);//set 0
kv_init(b->k_flag.a);//set 0
kv_init(b->sp);//set 0
if(!is_ug) b->ab = ha_abuf_init_buf(km);
else b->abl = ha_abufl_init_buf(km);
if (!b->is_final) {
init_Cigar_record_buf(&b->cigar1, km);
// init_Graph(&b->POA_Graph);
// init_Graph(&b->DAGCon);
init_Correct_dumy_buf(&b->correct, km);//set 0
InitHaplotypeEvdience_buf(&b->hap, km);
init_Round2_alignment_buf(&b->round2, km);
}
return b;
}
ha_ovec_buf_t *ha_ovec_init(int is_final, int save_ov, int is_ug)
{
ha_ovec_buf_t *b;
@@ -518,6 +550,17 @@ int64_t ha_ovec_mem(const ha_ovec_buf_t *b)
return mem;
}
uint32_t get_het_cnt(haplotype_evdience_alloc *hap)
{
uint32_t i, cnt;
for (i = cnt = 0; i < hap->snp_stat.n; i++) {
if(hap->snp_stat.a[i].score == 1 && (!(hap->snp_stat.a[i].occ_0 < 2 || hap->snp_stat.a[i].occ_1 < 2))) {
cnt++;
}
}
return cnt;
}
static void worker_ovec(void *data, long i, int tid)
{
ha_ovec_buf_t *b = ((ha_ovec_buf_t**)data)[tid];
@@ -559,6 +602,8 @@ static void worker_ovec(void *data, long i, int tid)
push_overlaps(&(R_INF.paf[i]), &b->olist, 1, &R_INF, is_rev);
push_overlaps(&(R_INF.reverse_paf[i]), &b->olist, 2, &R_INF, is_rev);
}
if(het_cnt) het_cnt[i] = get_het_cnt(&b->hap);
}
@@ -814,6 +859,20 @@ void rescue_hp_reads(ha_ovec_buf_t **b)
}
void print_het_cnt_log(uint32_t *het_cnt)
{
if(!het_cnt) return;
char* gfa_name = (char*)malloc(strlen(asm_opt.output_file_name)+35);
sprintf(gfa_name, "%s.het_cnt.log", asm_opt.output_file_name);
FILE* output_file = fopen(gfa_name, "w");
fprintf(stderr, "[M::%s::] ==> print cnt of het sites to %s...\n", __func__, gfa_name);
free(gfa_name);
uint64_t i;
for (i = 0; i < R_INF.total_reads; i++){
fprintf(output_file, ">%.*s\t%u\n", (int)Get_NAME_LENGTH(R_INF, i), Get_NAME(R_INF, i), het_cnt[i]);
}
fclose(output_file);
}
void ha_overlap_and_correct(int round)
@@ -838,6 +897,8 @@ void ha_overlap_and_correct(int round)
///debug_adapter(&asm_opt, &R_INF);
if (round == 0 && ha_flt_tab == 0) // then asm_opt.hom_cov hasn't been updated
ha_opt_update_cov(&asm_opt, hom_cov);
het_cnt = NULL;
if(round == asm_opt.number_of_round-1 && asm_opt.is_dbg_het_cnt) CALLOC(het_cnt, R_INF.total_reads);
if (asm_opt.required_read_name)
kt_for(asm_opt.thread_num, worker_ovec_related_reads, b, R_INF.total_reads);
else
@@ -847,6 +908,10 @@ void ha_overlap_and_correct(int round)
ha_pt_destroy(ha_idx);
ha_idx = NULL;
if(het_cnt) {
print_het_cnt_log(het_cnt); free(het_cnt); het_cnt = NULL;
}
// collect statistics
for (i = 0; i < asm_opt.thread_num; ++i) {
asm_opt.num_bases += b[i]->num_read_base;