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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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Correct.h
+58 -18
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@@ -6,6 +6,7 @@
#include "POA.h"
#include "Process_Read.h"
#include "Correct.h"
#include "kalloc.h"
//#define CORRECT_THRESHOLD 0.70
#define CORRECT_THRESHOLD 0.60
@@ -132,6 +133,7 @@ typedef struct
uint32_t overlapSite;
///there are several types: 0: equal to read 1: not equal to read, but it is a mismatch 2: is a gap
uint8_t type;
uint32_t cov;
///misbase
char misBase;
}haplotype_evdience;
@@ -790,10 +792,11 @@ inline int calculate_score(int new_occ_0, int new_occ_1)
return consensus;
}
inline void SetSnpMatrix(haplotype_evdience_alloc* h, uint32_t *nn_snp, uint64_t *overlap_num, int32_t set_matrix)
inline void SetSnpMatrix(haplotype_evdience_alloc* h, uint32_t *nn_snp, uint64_t *overlap_num, int32_t set_matrix, void *km)
{
if(nn_snp && overlap_num) {
kv_resize(SnpStats, h->snp_stat, *nn_snp);
if(!km) kv_resize(SnpStats, h->snp_stat, *nn_snp);
else kv_resize_km(km, SnpStats, h->snp_stat, *nn_snp);
h->snp_stat.n = 0; h->overlap = *overlap_num; h->core_snp = 0;
}
@@ -803,13 +806,15 @@ inline void SetSnpMatrix(haplotype_evdience_alloc* h, uint32_t *nn_snp, uint64_t
uint64_t new_size = n_snp* n_ovlp;
if(h->snp_matrix_size < new_size) {
h->snp_matrix_size = new_size;
REALLOC(h->snp_matrix, h->snp_matrix_size);
if(!km) REALLOC(h->snp_matrix, h->snp_matrix_size);
else KREALLOC(km, h->snp_matrix, h->snp_matrix_size);
}
memset(h->snp_matrix, -1, n_snp * n_ovlp);
if(h->r_snp_size < n_ovlp) {
h->r_snp_size = n_ovlp;
REALLOC(h->r_snp, h->r_snp_size);
if(!km) REALLOC(h->r_snp, h->r_snp_size);
else KREALLOC(km, h->r_snp, h->r_snp_size);
}
}
}
@@ -923,6 +928,18 @@ inline void init_DP_matrix(DP_matrix* dp, uint32_t snp_num)
}
inline void InitHaplotypeEvdience_buf(haplotype_evdience_alloc* h, void *km)
{
memset(h, 0, sizeof(haplotype_evdience_alloc));
/****************************may have bugs********************************/
memset(h->flag, 0, WINDOW_MAX_SIZE * sizeof(uint8_t));
/****************************may have bugs********************************/
// init_SNP_IDs(&(h->dp.SNP_IDs));
memset(&(h->dp.SNP_IDs), 0, sizeof(h->dp.SNP_IDs));
h->dp.SNP_IDs.max_snp_id = -1;
}
inline void InitHaplotypeEvdience(haplotype_evdience_alloc* h)
{
@@ -969,7 +986,6 @@ inline void InitHaplotypeEvdience(haplotype_evdience_alloc* h)
h->dp.max_buffer = NULL;
init_SNP_IDs(&(h->dp.SNP_IDs));
}
inline void StarSubListHaplotypeEvdience(haplotype_evdience_alloc* h)
@@ -1001,6 +1017,29 @@ inline void destoryHaplotypeEvdience(haplotype_evdience_alloc* h)
destory_SNP_IDs(&(h->dp.SNP_IDs));
}
inline void destoryHaplotypeEvdience_buf(void *km, haplotype_evdience_alloc* h, int is_z)
{
kfree(km, h->list);
kfree(km, h->snp_stat.a);
kfree(km, h->snp_srt.a);
kfree(km, h->snp_matrix);
kfree(km, h->r_snp);
kfree(km, h->dp.backtrack);
kfree(km, h->dp.max);
kfree(km, h->dp.max_for_sort);
kfree(km, h->dp.visit);
kfree(km, h->dp.backtrack_length);
kfree(km, h->dp.buffer);
kfree(km, h->dp.max_buffer);
kfree(km, h->dp.SNP_IDs.buffer);
kfree(km, h->dp.SNP_IDs.IDs);
if(is_z) {
memset(h, 0, sizeof(*h));
memset(&(h->dp.SNP_IDs), 0, sizeof(h->dp.SNP_IDs));
h->dp.SNP_IDs.max_snp_id = -1;
}
}
inline void ResizeInitHaplotypeEvdience(haplotype_evdience_alloc* h)
{
// h->snp = 0;
@@ -1021,17 +1060,14 @@ inline void RsetInitHaplotypeEvdienceFlag(haplotype_evdience_alloc* h, long long
/****************************may have bugs********************************/
}
inline void addHaplotypeEvdience(haplotype_evdience_alloc* h, haplotype_evdience* ev)
inline void addHaplotypeEvdience(haplotype_evdience_alloc* h, haplotype_evdience* ev, void *km)
{
uint32_t new_length = h->length + 1;
if(new_length > h->size)
{
h->size = h->size * 2;
if(h->size < new_length)
{
h->size = new_length;
}
h->list = (haplotype_evdience*)realloc(h->list, sizeof(haplotype_evdience)*h->size);
if(h->length + 1 > h->size){
h->size = h->length + 1;
kroundup32(h->size);
if(!km) REALLOC(h->list, h->size);
else KREALLOC(km, h->list, h->size);
// h->list = (haplotype_evdience*)realloc(h->list, sizeof(haplotype_evdience)*h->size);
}
h->list[h->length] = (*ev);
@@ -1080,6 +1116,7 @@ typedef struct
}
Round2_alignment;
void init_Round2_alignment_buf(Round2_alignment* h, void *km);
void init_Round2_alignment(Round2_alignment* h);
void destory_Round2_alignment(Round2_alignment* h);
void clear_Round2_alignment(Round2_alignment* h);
@@ -1091,13 +1128,16 @@ void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
Cigar_record* current_cigar, haplotype_evdience_alloc* hap,
Round2_alignment* second_round, int force_repeat, int is_consensus,
int* fully_cov, int* abnormal);
void init_Correct_dumy_buf(Correct_dumy* list, void *km);
void init_Correct_dumy(Correct_dumy* list);
void destory_Correct_dumy(Correct_dumy* list);
void clear_Correct_dumy(Correct_dumy* list, overlap_region_alloc* overlap_list);
void destory_Correct_dumy_buf(void *km, Correct_dumy* list, int is_z);
void clear_Correct_dumy(Correct_dumy* list, overlap_region_alloc* overlap_list, void *km);
void clear_Correct_dumy_pure(Correct_dumy* list);
void get_seq_from_Graph(Graph* backbone, Graph* DAGCon, Correct_dumy* dumy, Cigar_record* current_cigar, char* self_string,
char* r_string, long long r_string_length, long long r_string_site);
void init_Cigar_record(Cigar_record* dummy);
void init_Cigar_record_buf(Cigar_record* dummy, void *km);
void destory_Cigar_record(Cigar_record* dummy);
void clear_Cigar_record(Cigar_record* dummy);
void add_new_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type);
@@ -1106,11 +1146,11 @@ void add_new_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint3
void add_existing_cell_to_cigar_record_with_different_base(Cigar_record* dummy, uint32_t len, uint32_t type, char* seq);
void correct_ul_overlap(overlap_region_alloc* overlap_list, const ma_ug_t *uref,
void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read,
Graph* g, Graph* DAGCon, Cigar_record* current_cigar,
haplotype_evdience_alloc* hap, Round2_alignment* second_round,
int force_repeat, int is_consensus, int* fully_cov, int* abnormal, double max_ov_diff_ec);
int force_repeat, int is_consensus, int* fully_cov, int* abnormal, double max_ov_diff_ec, void *km);
/***
type: