Update modimers

Assembly.cpp

@@ -75,7 +75,6 @@ void Verify_Counting()
 
 
 }
-/********************************for debug***************************************/
 
 
 
@@ -83,6 +82,10 @@ void Verify_Counting()
 void* Perform_Counting(void* arg)
 {
     int thr_ID = *((int*)arg);
+
+    ///debug_mode(101, thr_ID, thread_num);
+
+
     int i = 0;
     HPC_seq HPC_read;
 
@@ -91,6 +94,7 @@ void* Perform_Counting(void* arg)
     init_R_buffer_block(&curr_sub_block);
 
     long long read_number = 0;
+    long long select_k_mer_number = 0 ;
     long long k_mer_number = 0 ;
 
 	int file_flag = 1;
@@ -126,8 +130,13 @@ void* Perform_Counting(void* arg)
                     if (avalible_k>=k_mer_length)
                     {
                         ///插入
-                        insert_Total_Count_Table(&TCB, &k_code, k_mer_length);
+                        if(insert_Total_Count_Table(&TCB, &k_code, k_mer_length))
+                        {
+                            select_k_mer_number++;
+                        }
+
                         k_mer_number++;
+                        
                     }
                     
                 }
@@ -148,7 +157,8 @@ void* Perform_Counting(void* arg)
     destory_R_buffer_block(&curr_sub_block);
     free(arg);
 
-    fprintf(stdout, "thr_ID: %d, read_number: %lld, k_mer_number: %lld\n",thr_ID, read_number, k_mer_number);
+    fprintf(stdout, "thr_ID: %d, read_number: %lld, select_k_mer_number: %lld, k_mer_number: %lld\n",
+    thr_ID, read_number, select_k_mer_number, k_mer_number);
 
 }
 
@@ -167,7 +177,6 @@ void* Perform_Counting(void* arg)
 
 
 
-
 void Counting_multiple_thr()
 {
 

Assembly.h

@@ -6,6 +6,5 @@
 void Counting_multiple_thr();
 /********************************for debug***************************************/
 void Verify_Counting();
-/********************************for debug***************************************/
 
 #endif

Hash_Table.cpp

@@ -58,7 +58,27 @@ void destory_Total_Count_Table(Total_Count_Table* TCB)
 }
 
 
+/********************************for debug***************************************/
+void debug_mode(uint64_t d, uint64_t thread_ID, uint64_t thread_num)
+{
+    fprintf(stderr, "#%llu: Start debug_mode...\n", thread_ID);
 
+    uint64_t i;
+
+    for (i = thread_ID; i < 4,294,967,296; i = i + thread_num)
+    {
+        if(i%d != mod_d(0, i, d))
+        {
+            fprintf(stderr, "ERROR mode, i: %llu\n", i);
+            fprintf(stderr, "i mod d: %llu\n", i%d);
+            fprintf(stderr, "mod_d(0, i, d): %llu\n", mod_d(0, i, d));
+        }
+
+    }
+
+    fprintf(stderr, "#%llu: Finish debug_mode\n", thread_ID);
+    
+}
 
 
 /********************************for debug***************************************/
@@ -111,4 +131,3 @@ void test_COUNT64()
     
 
 }
-/********************************for debug***************************************/

Hash_Table.h

@@ -9,6 +9,7 @@ typedef khash_t(COUNT64) Count_Table;
 
 #define PREFIX_BITS 16
 #define MAX_SUFFIX_BITS 64
+#define MODE_VALUE 101
 
 typedef struct
 {
@@ -40,9 +41,20 @@ inline void print_64bit(uint64_t x)
 
     fprintf(stderr, "\n");
 }
-/********************************for debug***************************************/
 
-inline void get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, Hash_code* code, int k)
+inline uint64_t mod_d(uint64_t h_key, uint64_t low_key, uint64_t d)
+{
+    uint64_t result = (h_key >> 32) % d;
+    result = ((result << 32) + (h_key & (uint64_t)0xffffffff)) % d;
+    result = ((result << 32) + (low_key >> 32)) % d;
+    result = ((result << 32) + (low_key & (uint64_t)0xffffffff)) % d;
+
+    return result;
+}
+
+
+
+inline int get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Count_Table* TCB, 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
@@ -51,6 +63,12 @@ inline void get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Cou
     //k不可能为0, 所以这个右移不会有问题
     h_key = code->x[1] >> (64 - k);
 
+    if(mod_d(h_key, low_key, MODE_VALUE) > 3)
+    {
+        return 0;
+    }
+
+
     ///注意suffix_bits最大就是64
     ///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
@@ -61,13 +79,18 @@ inline void get_sub_table(uint64_t* get_sub_ID, uint64_t* get_sub_key, Total_Cou
     *get_sub_ID = sub_ID;
     *get_sub_key = sub_key;
 
+     return 1;
+
 }
 
 
-inline void insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
+inline int insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
 {
     uint64_t sub_ID, sub_key;
-    get_sub_table(&sub_ID, &sub_key, TCB, code, k);
+    if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
+    {
+        return 0;
+    }
 
     khint_t t;  ///这就是个迭代器
     int absent;
@@ -90,13 +113,18 @@ inline void insert_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, in
     }
 
     __sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
+
+    return 1;
 }
 
 inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
 {
 
     uint64_t sub_ID, sub_key;
-    get_sub_table(&sub_ID, &sub_key, TCB, code, k);
+    if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
+    {
+        return 0;
+    }
 
     khint_t t;  ///这就是个迭代器
     int absent;
@@ -113,13 +141,18 @@ inline int get_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
         return -1;
     }
 
+    return 1;
+
 }
 
 /********************************for debug***************************************/
 inline int verify_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int k)
 {
     uint64_t sub_ID, sub_key;
-    get_sub_table(&sub_ID, &sub_key, TCB, code, k);
+    if(!get_sub_table(&sub_ID, &sub_key, TCB, code, k))
+    {
+        return 0;
+    }
 
     khint_t t;  ///这就是个迭代器
     int absent;
@@ -144,7 +177,6 @@ inline int verify_Total_Count_Table(Total_Count_Table* TCB, Hash_code* code, int
         return -1;
     }
 }
-/********************************for debug***************************************/
 
 /********************************for debug***************************************/
 inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
@@ -174,7 +206,6 @@ inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
     
     fprintf(stdout, "non_empty_k_mer: %lld\n", non_empty_k_mer);
 }
-/********************************for debug***************************************/
 
 
 void init_Total_Count_Table(int k, Total_Count_Table* TCB);
@@ -184,6 +215,9 @@ void init_Count_Table(Count_Table** table);
 
 /********************************for debug***************************************/
 void test_COUNT64();
+
 /********************************for debug***************************************/
+void debug_mode(uint64_t d, uint64_t thread_ID, uint64_t thread_num);
+
 
 #endif

main.cpp

@@ -13,7 +13,6 @@ void debug_Counting()
     fprintf(stderr, "debug over!\n");
     destory_kseq();
 }
-/********************************for debug***************************************/
 
 
 int main(int argc, char *argv[])