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smaller memory requirement

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chhylp123
2022-05-12 16:15:58 -04:00
parent dd8888aa90
commit a2198891e7
8 changed files with 1345 additions and 2581 deletions
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Correct.h
+15 -27
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@@ -1017,28 +1017,6 @@ 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)
{
@@ -1126,12 +1104,11 @@ void clear_Round2_alignment(Round2_alignment* h);
void correct_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
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);
Round2_alignment* second_round, kvec_t_u64_warp* v_idx, window_list_alloc* win_ciagr_buf,
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 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,
@@ -1150,6 +1127,7 @@ 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,
kvec_t_u64_warp* v_idx, window_list_alloc* win_ciagr_buf,
int force_repeat, int is_consensus, int* fully_cov, int* abnormal,
double max_ov_diff_ec, long long winLen, void *km);
@@ -1253,8 +1231,8 @@ long long* max_q_pos, long long* max_t_pos, long long* global_score,
long long* extention_score, long long* q_boundary_score, long long* q_boundary_t_coordinate,
long long* t_boundary_score, long long* t_boundary_q_coordinate,
long long* droped, int mode);
void correct_overlap_high_het(overlap_region_alloc* overlap_list, All_reads* R_INF,
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read);
// void correct_overlap_high_het(overlap_region_alloc* overlap_list, All_reads* R_INF,
// UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read);
long long get_affine_gap_score(overlap_region* ovc, UC_Read* g_read, UC_Read* overlap_read, uint8_t* x_num,
uint8_t* y_num, uint64_t EstimateXOlen, uint64_t EstimateYOlen);
int collect_hp_regions(overlap_region_alloc* olist, All_reads* R_INF, kvec_t_u8_warp* k_flag, float hp_rate, int rlen, FILE* fp);
@@ -1271,7 +1249,17 @@ inline int if_exact_match(char* x, long long xLen, char* y, long long yLen, long
return 0;
}
inline void get_cigar_cell(window_list *idx, window_list_alloc *cc, uint32_t i, uint8_t *c, uint32_t *len)
{
uint32_t p = cc->c.a[idx->cidx+i];
(*c) = (uint8_t)(p>>30); (*len) = (p<<2)>>2;
}
inline void push_cigar_cell(window_list_alloc *res, uint8_t c, uint32_t len)
{
uint32_t p = c; p <<= 30; p += len;
kv_push(uint32_t, res->c, p);
}
#define FORWARD_KSW 0
#define BACKWARD_KSW 1