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Update position hash table

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This commit is contained in:
Haoyu Cheng
2019-05-14 17:02:03 -04:00
parent df18b5af76
commit 45355a1103
17 changed files with 878 additions and 120 deletions
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Hash_Table.h
+215 -14
View File
@@ -4,13 +4,16 @@
#include "kmer.h"
KHASH_MAP_INIT_INT64(COUNT64, int)
typedef khash_t(COUNT64) Count_Table;
KHASH_MAP_INIT_INT64(POS64, uint64_t)
typedef khash_t(POS64) Pos_Table;
#define PREFIX_BITS 16
#define MAX_SUFFIX_BITS 64
#define MODE_VALUE 101
typedef struct
{
volatile int lock;
@@ -25,8 +28,30 @@ typedef struct
int suffix_bits;
int size;
uint64_t suffix_mode;
uint64_t non_unique_k_mer;
} Total_Count_Table;
typedef struct
{
uint64_t offset;
uint64_t readID;
} k_mer_pos;
typedef struct
{
Pos_Table** sub_h;
Hash_table_spin_lock* sub_h_lock;
int prefix_bits;
int suffix_bits;
int size;
uint64_t suffix_mode;
k_mer_pos* pos;
uint64_t useful_k_mer;
uint64_t total_occ;
uint64_t* k_mer_index;
} Total_Pos_Table;
/********************************for debug***************************************/
inline void print_64bit(uint64_t x)
{
@@ -54,7 +79,9 @@ inline uint64_t mod_d(uint64_t h_key, uint64_t low_key, uint64_t d)
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, 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,
Hash_code* code, int k)
{
uint64_t h_key, low_key;
///k有可能是64，所以可能会有问题
@@ -73,8 +100,8 @@ inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Coun
///前一个右移不安全，因为TCB->suffix_bits有可能为64
///后一个左移安全，因为TCB->suffix_bits不可能为0
//uint64_t sub_ID = (low_key >> TCB->suffix_bits) | (h_key << (64 - TCB->suffix_bits));
uint64_t sub_ID = (low_key >> SAFE_SHIFT(TCB->suffix_bits)) | (h_key << (64 - TCB->suffix_bits));
uint64_t sub_key = (low_key & TCB->suffix_mode);
uint64_t sub_ID = (low_key >> SAFE_SHIFT(suffix_bits)) | (h_key << (64 - suffix_bits));
uint64_t sub_key = (low_key & suffix_mode);
*get_sub_ID = sub_ID;
*get_sub_key = sub_key;
@@ -87,7 +114,7 @@ inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Coun
inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
{
uint64_t sub_ID, sub_key;
if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
{
return 0;
}
@@ -121,7 +148,7 @@ inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
{
uint64_t sub_ID, sub_key;
if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
{
return 0;
}
@@ -138,18 +165,192 @@ inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
}
else
{
return -1;
return 0;
}
return 1;
}
inline uint64_t get_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t* r_sub_ID)
{
uint64_t sub_ID, sub_key;
if(!get_sub_table(&sub_ID, &sub_key, PCB->suffix_mode, PCB->suffix_bits, code, k))
{
return (uint64_t)-1;
}
khint_t t; ///这就是个迭代器
int absent;
///查询哈希表，key为k
t = kh_get(POS64, PCB->sub_h[sub_ID], sub_key);
if (t != kh_end(PCB->sub_h[sub_ID]))
{
*r_sub_ID = sub_ID;
return kh_value(PCB->sub_h[sub_ID], t);
}
else
{
return (uint64_t)-1;
}
}
inline uint64_t count_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k)
{
uint64_t sub_ID;
uint64_t ret = get_Total_Pos_Table(PCB, code, k, &sub_ID);
if(ret != (uint64_t)-1)
{
return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
}
else
{
return 0;
}
}
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)
{
uint64_t ret = get_Total_Pos_Table(PCB, code, k, r_sub_ID);
if(ret != (uint64_t)-1)
{
*list = PCB->k_mer_index[ret] + PCB->pos;
return PCB->k_mer_index[ret + 1] - PCB->k_mer_index[ret];
}
else
{
*list = NULL;
return 0;
}
}
int cmp_k_mer_pos(const void * a, const void * b);
inline uint64_t insert_Total_Pos_Table(Total_Pos_Table* PCB, Hash_code* code, int k, uint64_t readID, uint64_t pos)
{
k_mer_pos* list;
int flag = 0;
uint64_t sub_ID;
uint64_t occ = locate_Total_Pos_Table(PCB, code, &list, k, &sub_ID);
if (occ)
{
while (__sync_lock_test_and_set(&PCB->sub_h_lock[sub_ID].lock, 1))
{
while (PCB->sub_h_lock[sub_ID].lock);
}
if (list[0].offset + 1 < occ)
{
list[0].offset++;
list[list[0].offset].readID = readID;
list[list[0].offset].offset = pos;
}
else
{
list[0].readID = readID;
list[0].offset = pos;
flag = 1;
}
__sync_lock_release(&PCB->sub_h_lock[sub_ID].lock);
///当所有位置都存好后，不会再有其他线程修改该list
///所以可以在临界区外排序
if (flag && occ>1)
{
qsort(list, occ, sizeof(k_mer_pos), cmp_k_mer_pos);
}
return 1;
}
else
{
return 0;
}
}
void init_Total_Count_Table(int k, Total_Count_Table* TCB);
void init_Total_Pos_Table(Total_Pos_Table* TCB, Total_Count_Table* pre_TCB);
void destory_Total_Count_Table(Total_Count_Table* TCB);
void init_Count_Table(Count_Table** table);
void init_Pos_Table(Count_Table** pre_table, Pos_Table** table);
void Traverse_Counting_Table(Total_Count_Table* TCB, Total_Pos_Table* PCB, int k_mer_min_freq, int k_mer_max_freq);
/********************************for debug***************************************/
inline int verify_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
{
uint64_t sub_ID, sub_key;
if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
if(!get_sub_table(&sub_ID, &sub_key, TCB->suffix_mode, TCB->suffix_bits, code, k))
{
return 0;
}
@@ -178,6 +379,11 @@ inline int verify_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int
}
}
/********************************for debug***************************************/
inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
{
@@ -208,11 +414,6 @@ inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
}
void init_Total_Count_Table(int k, Total_Count_Table* TCB);
void destory_Total_Count_Table(Total_Count_Table* TCB);
void init_Count_Table(Count_Table** table);
/********************************for debug***************************************/
void test_COUNT64();