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backup without bundaries processing

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This commit is contained in:
Haoyu Cheng
2019-12-17 16:58:20 -05:00
parent 90195293f1
commit 06556e4a9b
7 changed files with 2227 additions and 394 deletions
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Hash_Table.h
+44 -2
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@@ -100,6 +100,14 @@ typedef struct
} window_list;
typedef struct
{
window_list* buffer;
long long length;
long long size;
}window_list_alloc;
typedef struct
{
uint64_t* buffer;
@@ -133,6 +141,8 @@ typedef struct
uint64_t w_list_length;
int8_t strong;
Fake_Cigar f_cigar;
window_list_alloc boundary_cigars;
} overlap_region;
@@ -250,7 +260,25 @@ inline int if_k_mer_available(Hash_code* code, int k)
return 1;
}
////suffix_bits = 64 in default
inline int recover_hash_code(uint64_t sub_ID, uint64_t sub_key, Hash_code* code,
uint64_t suffix_mode, int suffix_bits, int k)
{
uint64_t h_key, low_key;
h_key = low_key = 0;
low_key = sub_ID << SAFE_SHIFT(suffix_bits);
low_key = low_key | sub_key;
h_key = sub_ID >> (64 - suffix_bits);
code->x[0] = code->x[1] = 0;
uint64_t mask = ALL >> (64 - k);
code->x[0] = low_key & mask;
code->x[1] = h_key << (64 - k);
code->x[1] = code->x[1] | (low_key >> SAFE_SHIFT(k));
}
///inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, Hash_code* code, int k)
inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, uint64_t suffix_mode, int suffix_bits,
@@ -279,7 +307,13 @@ Hash_code* code, int k)
*get_sub_ID = sub_ID;
*get_sub_key = sub_key;
return 1;
// Hash_code de_code;
// recover_hash_code(sub_ID, sub_key, &de_code, suffix_mode, suffix_bits, k);
///if(de_code.x[0] != (*code).x[0] || de_code.x[1] != (*code).x[1]) fprintf(stderr, "hehe\n");
///if(de_code.x[0] == (*code).x[0] || de_code.x[1] == (*code).x[1]) fprintf(stderr, "hehe\n");
return 1;
}
@@ -514,7 +548,7 @@ void calculate_inexact_overlap_region(Candidates_list* candidates, overlap_regio
uint64_t readID, uint64_t readLength, All_reads* R_INF);
void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold);
uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end);
@@ -703,4 +737,12 @@ void append_overlap_region_alloc_from_existing(overlap_region_alloc* list, overl
int cmp_by_x_pos_s(const void * a, const void * b);
void resize_Chain_Data(Chain_Data* x, long long size);
void init_window_list_alloc(window_list_alloc* x);
void clear_window_list_alloc(window_list_alloc* x);
void destory_window_list_alloc(window_list_alloc* x);
void resize_window_list_alloc(window_list_alloc* x, long long size);
#endif