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resure alignment

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This commit is contained in:
Haoyu Cheng
2019-07-12 10:18:25 -04:00
parent 3d88530385
commit f508762557
7 changed files with 1030 additions and 264 deletions
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Hash_Table.h
+33 -2
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@@ -13,6 +13,14 @@ typedef khash_t(POS64) Pos_Table;
#define MAX_SUFFIX_BITS 64
#define MODE_VALUE 101
///#define WINDOW 350
///#define THRESHOLD 14
#define WINDOW 375
#define THRESHOLD 15
#define THRESHOLD_RATE 0.04
#define GROUP_SIZE 4
///最长是10M10D10M10D10M这种
#define CIGAR_MAX_LENGTH THRESHOLD*2+2
typedef struct
{
@@ -53,6 +61,26 @@ typedef struct
uint64_t length;
} k_mer_pos_list_alloc;
typedef struct
{
int C_L[CIGAR_MAX_LENGTH];
char C_C[CIGAR_MAX_LENGTH];
int length;
} CIGAR;
typedef struct
{
uint64_t x_start;
uint64_t x_end;
int y_end;
int y_start;
///int y_pre_start;
///error小于等于0都要重新算
int error;
CIGAR cigar;
} window_list;
typedef struct
{
uint64_t x_id;
@@ -67,6 +95,10 @@ typedef struct
uint64_t shared_seed;
uint64_t align_length;
window_list* w_list;
uint64_t w_list_size;
uint64_t w_list_length;
} overlap_region;
@@ -406,8 +438,7 @@ void destory_overlap_region_alloc(overlap_region_alloc* list);
void append_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp, All_reads* R_INF);
void calculate_overlap_region(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF);
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error);