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2019_9_5

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This commit is contained in:
Haoyu Cheng
2019-09-05 11:47:54 -04:00
parent d5327fe9ee
commit b57923d050
6 changed files with 876 additions and 137 deletions
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Correct.h
+20 -2
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@@ -6,7 +6,7 @@
#include "POA.h"
#include "Process_Read.h"
#define CORRECT_THRESHOLD 0.7
#define CORRECT_THRESHOLD 0.70
#define MIN_COVERAGE_THRESHOLD 4
#define CORRECT_INDEL_LENGTH 2
#define MISMATCH 1
@@ -335,6 +335,7 @@ typedef struct
{
char* corrected_read;
long long corrected_read_length;
long long last_boundary_length;
long long corrected_read_size;
long long corrected_base;
@@ -351,15 +352,31 @@ typedef struct
__m128i Peq_SSE[256];
} Correct_dumy;
typedef struct
{
Correct_dumy dumy;
Cigar_record cigar;
Cigar_record tmp_cigar;
long long obtained_cigar_length;
}
Round2_alignment;
void init_Round2_alignment(Round2_alignment* h);
void destory_Round2_alignment(Round2_alignment* h);
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,
long long* matched_overlap_0, long long* matched_overlap_1,
long long* potiental_matched_overlap_0, long long* potiental_matched_overlap_1,
Cigar_record* current_cigar, haplotype_evdience_alloc* hap);
Cigar_record* current_cigar, haplotype_evdience_alloc* hap,
Round2_alignment* second_round);
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 clear_Correct_dumy_pure(Correct_dumy* list);
void pre_filter_by_nearby(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read,
All_reads* R_INF, Correct_dumy* dumy, uint64_t* new_n_length);
void pre_filter_by_nearby_single(k_mer_pos* new_n_list, k_mer_pos* old_n_list, uint64_t n_length, uint64_t n_end_pos, UC_Read* g_read,
@@ -372,6 +389,7 @@ void clear_Cigar_record(Cigar_record* dummy);
inline void add_new_cell_to_cigar_record(Cigar_record* dummy, uint32_t len, uint32_t type)
{
uint32_t tmp;