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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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Hash_Table.h
+20 -23
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@@ -44,32 +44,29 @@ typedef struct
uint64_t end_pos;
} k_mer_pos_list;
typedef struct
{
int C_L[CIGAR_MAX_LENGTH];
char C_C[CIGAR_MAX_LENGTH];
int length;
} CIGAR;
// typedef struct
// {
// int C_L[CIGAR_MAX_LENGTH];
// char C_C[CIGAR_MAX_LENGTH];
// int length;
// } CIGAR;
typedef struct
{
///the begining and end of a window, instead of the whole overlap
uint64_t x_start;
uint64_t x_end;
int y_end;
int y_start;
int extra_begin;
int extra_end;
int error_threshold;
int error;
CIGAR cigar;
int32_t x_start, x_end;
int32_t y_start, y_end;
int32_t extra_begin, extra_end;
int32_t error, error_threshold;
uint32_t cidx, clen;
//CIGAR cigar;
} window_list;
typedef struct
{
window_list* buffer;
int32_t length;
int32_t size;
size_t n, m;
window_list *a;
kvec_t(uint32_t) c;
} window_list_alloc;
typedef struct
@@ -100,11 +97,12 @@ typedef struct
int8_t strong;
uint32_t non_homopolymer_errors;
window_list* w_list;
uint32_t w_list_size;
uint32_t w_list_length;
// window_list* w_list;
// uint32_t w_list_size;
// uint32_t w_list_length;
Fake_Cigar f_cigar;
window_list_alloc w_list;
window_list_alloc boundary_cigars;
} overlap_region;
@@ -149,7 +147,6 @@ void destory_Candidates_list_buf(void *km, Candidates_list* l, int is_z);
void init_overlap_region_alloc(overlap_region_alloc* list);
void clear_overlap_region_alloc(overlap_region_alloc* list);
void destory_overlap_region_alloc(overlap_region_alloc* list);
void destory_overlap_region_alloc_buf(void *km, overlap_region_alloc* list, int is_z);
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
int extra_begin, int extra_end, int error_threshold, int blockLen, void *km);
@@ -196,7 +193,7 @@ void resize_Chain_Data(Chain_Data* x, long long size, void *km);
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, void *km);
void resize_window_list_alloc(window_list_alloc* x, uint64_t size);
long long chain_DP(k_mer_hit* a, long long a_n, Chain_Data* dp, overlap_region* result, double band_width_threshold, int max_skip, int x_readLen, int y_readLen, void *km);
int append_utg_inexact_overlap_region_alloc(overlap_region_alloc* list, overlap_region* tmp,
ma_utg_v *ua, int add_beg_end, void *km);