mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-08 02:58:12 +08:00
removed hifiasm hash table index
This commit is contained in:
Heng Li
+1
-209
@@ -33,23 +33,6 @@ KHASHL_MAP_INIT(static inline, Pos_Table, ha_pt, uint64_t, uint64_t, kh_hash_dum
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///#define CIGAR_MAX_LENGTH THRESHOLD*2+2
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#define CIGAR_MAX_LENGTH 31*2+4
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typedef struct
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{
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volatile int lock;
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} Hash_table_spin_lock;
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typedef struct
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{
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Count_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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///number of subtable
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int size;
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uint64_t suffix_mode;
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uint64_t non_unique_k_mer;
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} Total_Count_Table;
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typedef struct
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{
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uint32_t offset;
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@@ -187,21 +170,6 @@ typedef struct
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Chain_Data chainDP;
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} Candidates_list;
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typedef struct
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{
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Pos_Table** sub_h;
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Hash_table_spin_lock* sub_h_lock;
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int prefix_bits;
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int suffix_bits;
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///number of subtable
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int size;
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uint64_t suffix_mode;
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k_mer_pos* pos;
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uint64_t useful_k_mer;
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uint64_t total_occ;
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uint64_t* k_mer_index;
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} Total_Pos_Table;
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////suffix_bits = 64 in default
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inline int recover_hash_code(uint64_t sub_ID, uint64_t sub_key, Hash_code* code,
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uint64_t suffix_mode, int suffix_bits, int k) // FIXME: not working right now
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@@ -258,204 +226,29 @@ inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, uint64_t s
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return ha_get_sub_table_long(get_sub_ID, get_sub_key, suffix_mode, suffix_bits, code, k);
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}
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inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t;
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int absent;
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while (__sync_lock_test_and_set(&TCB->sub_h_lock[sub_ID].lock, 1))
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{
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while (TCB->sub_h_lock[sub_ID].lock);
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}
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t = ha_ct_put(TCB->sub_h[sub_ID], sub_key, &absent);
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if (absent)
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{
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kh_val(TCB->sub_h[sub_ID], t) = 1;
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}
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else
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{
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//kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1;
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kh_val(TCB->sub_h[sub_ID], t)++;
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}
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__sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
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return 1;
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}
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inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
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{
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return 0;
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}
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khint_t t;
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t = ha_ct_get(TCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(TCB->sub_h[sub_ID]))
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{
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return kh_val(TCB->sub_h[sub_ID], t);
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}
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else
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{
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return 0;
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}
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}
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inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t* r_sub_ID)
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{
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uint64_t sub_ID, sub_key;
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if(!get_sub_table(&sub_ID, &sub_key, PCB->suffix_mode, PCB->suffix_bits, code, k))
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{
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return (uint64_t)-1;
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}
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khint_t t;
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t = ha_pt_get(PCB->sub_h[sub_ID], sub_key);
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if (t != kh_end(PCB->sub_h[sub_ID]))
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{
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*r_sub_ID = sub_ID;
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return kh_val(PCB->sub_h[sub_ID], t);
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}
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else
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{
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return (uint64_t)-1;
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}
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}
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inline uint64_t count_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k)
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{
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uint64_t sub_ID;
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uint64_t ret = get_Total_Pos_Table(PCB, code, k, &sub_ID);
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if(ret != (uint64_t)-1)
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{
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return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
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}
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else
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{
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return 0;
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}
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}
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inline uint64_t locate_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, k_mer_pos** list, int k, uint64_t* r_sub_ID)
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{
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uint64_t ret = get_Total_Pos_Table(PCB, code, k, r_sub_ID);
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if(ret != (uint64_t)-1)
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{
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*list = PCB->k_mer_index[ret] + PCB->pos;
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return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
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}
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else
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{
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*list = NULL;
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return 0;
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}
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}
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int cmp_k_mer_pos(const void * a, const void * b);
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inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos)
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{
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k_mer_pos* list;
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int flag = 0;
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uint64_t sub_ID;
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uint64_t occ = locate_Total_Pos_Table(PCB, code, &list, k, &sub_ID);
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if (occ)
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{
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while (__sync_lock_test_and_set(&PCB->sub_h_lock[sub_ID].lock, 1))
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{
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while (PCB->sub_h_lock[sub_ID].lock);
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}
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if (list[0].offset + 1 < occ)
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{
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list[0].offset++; // if not the last k-mer, this field is reused to keep the number of inserted positions
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list[list[0].offset].readID = readID;
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list[list[0].offset].offset = pos;
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list[list[0].offset].rev = ha_code2rev(code);
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}
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else // now comes to the last k-mer position; then save it to list[0]
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{
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list[0].readID = readID;
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list[0].offset = pos;
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list[0].rev = ha_code2rev(code);
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flag = 1;
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}
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__sync_lock_release(&PCB->sub_h_lock[sub_ID].lock);
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//if all pos has been saved, it is safe to sort
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if (flag && occ>1)
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{
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qsort(list, occ, sizeof(k_mer_pos), cmp_k_mer_pos);
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}
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return 1;
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}
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else
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{
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return 0;
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}
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}
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void init_Total_Count_Table(int k, Total_Count_Table* TCB);
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void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB);
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void destory_Total_Count_Table(Total_Count_Table* TCB);
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void init_Count_Table(Count_Table** table);
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void init_Pos_Table(Count_Table** pre_table, Pos_Table** table);
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void destory_Total_Pos_Table(Total_Pos_Table* TCB);
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void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
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int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
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void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq);
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void init_Candidates_list(Candidates_list* l);
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void clear_Candidates_list(Candidates_list* l);
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void destory_Candidates_list(Candidates_list* l);
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void init_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
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void destory_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
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void clear_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list);
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void append_k_mer_pos_list_alloc(k_mer_pos_list_alloc* list, k_mer_pos* n_list, uint64_t n_length,
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uint64_t n_end_pos, uint8_t n_direction);
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void init_overlap_region_alloc(overlap_region_alloc* list);
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void clear_overlap_region_alloc(overlap_region_alloc* list);
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void destory_overlap_region_alloc(overlap_region_alloc* list);
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void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
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int extra_begin, int extra_end, int error_threshold);
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void overlap_region_sort_y_id(overlap_region *a, long long n);
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void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_region_alloc* overlap_list,
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uint64_t readID, uint64_t readLength, All_reads* R_INF, double band_width_threshold, int add_beg_end);
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void init_fake_cigar(Fake_Cigar* x);
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void destory_fake_cigar(Fake_Cigar* x);
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void clear_fake_cigar(Fake_Cigar* x);
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@@ -463,6 +256,7 @@ void add_fake_cigar(Fake_Cigar* x, uint32_t gap_site, int32_t gap_shift);
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void resize_fake_cigar(Fake_Cigar* x, uint64_t size);
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int get_fake_gap_pos(Fake_Cigar* x, int index);
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int get_fake_gap_shift(Fake_Cigar* x, int index);
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inline long long y_start_offset(long long x_start, Fake_Cigar* o)
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{
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if(x_start == get_fake_gap_pos(o, o->length - 1))
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@@ -470,7 +264,6 @@ inline long long y_start_offset(long long x_start, Fake_Cigar* o)
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return get_fake_gap_shift(o, o->length - 1);
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}
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long long i;
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for (i = 0; i < (long long)o->length; i++)
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{
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@@ -508,5 +301,4 @@ void clear_window_list_alloc(window_list_alloc* x);
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void destory_window_list_alloc(window_list_alloc* x);
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void resize_window_list_alloc(window_list_alloc* x, long long size);
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#endif
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