Finish multiple thread counting

Hash_Table.h

@@ -0,0 +1,189 @@
+#ifndef __HASHTABLE__
+#define __HASHTABLE__
+#include "khash.h"
+#include "kmer.h"
+
+KHASH_MAP_INIT_INT64(COUNT64, int) 
+
+typedef khash_t(COUNT64) Count_Table;
+
+#define PREFIX_BITS 16
+#define MAX_SUFFIX_BITS 64
+
+typedef struct
+{
+    volatile int lock;
+
+}Hash_table_spin_lock;
+
+typedef struct
+{
+	Count_Table** sub_h;
+    Hash_table_spin_lock* sub_h_lock;
+    int prefix_bits;
+    int suffix_bits;
+	int size;
+    uint64_t suffix_mode;
+} Total_Count_Table;
+
+/********************************for debug***************************************/
+inline void print_64bit(uint64_t x)
+{
+    int i;
+    for(i = 63; i >= 0; i--)
+	{
+		if(x & ((1ULL<<i)))
+			fprintf(stderr, "1");
+		else
+			fprintf(stderr, "0");
+	}
+
+    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)
+{
+    uint64_t h_key, low_key;
+    ///k有可能是64，所以可能会有问题
+    ///low_key = code->x[0] | (code->x[1] << k);
+    low_key = code->x[0] | (code->x[1] << SAFE_SHIFT(k));
+    //k不可能为0, 所以这个右移不会有问题
+    h_key = code->x[1] >> (64 - k);
+
+    ///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
+    //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);
+
+    *get_sub_ID = sub_ID;
+    *get_sub_key = sub_key;
+
+}
+
+
+inline void 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);
+
+    khint_t t;  ///这就是个迭代器
+    int absent;
+
+
+    while (__sync_lock_test_and_set(&TCB->sub_h_lock[sub_ID].lock, 1))
+    {
+        while (TCB->sub_h_lock[sub_ID].lock);
+    }
+
+    t = kh_put(COUNT64, TCB->sub_h[sub_ID], sub_key, &absent);
+    if (absent)
+    {
+        kh_value(TCB->sub_h[sub_ID], t) = 1;
+    }
+    else   ///哈希表中已有的元素
+    {
+        //kh_value(TCB->sub_h[sub_ID], t) = kh_value(TCB->sub_h[sub_ID], t) + 1;
+        kh_value(TCB->sub_h[sub_ID], t)++;
+    }
+
+    __sync_lock_release(&TCB->sub_h_lock[sub_ID].lock);
+}
+
+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);
+
+    khint_t t;  ///这就是个迭代器
+    int absent;
+
+    ///查询哈希表，key为k
+    t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
+
+    if (t != kh_end(TCB->sub_h[sub_ID]))
+    {
+        return kh_value(TCB->sub_h[sub_ID], t);
+    }
+    else
+    {
+        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);
+
+    khint_t t;  ///这就是个迭代器
+    int absent;
+
+    ///查询哈希表，key为k
+    t = kh_get(COUNT64, TCB->sub_h[sub_ID], sub_key);
+
+    if (t != kh_end(TCB->sub_h[sub_ID]))
+    {
+        kh_value(TCB->sub_h[sub_ID], t)--;
+        if (kh_value(TCB->sub_h[sub_ID], t)<0)
+        {
+           return -1;
+        }
+        else
+        {
+            return 1;
+        }
+    }
+    else
+    {
+        return -1;
+    }
+}
+/********************************for debug***************************************/
+
+/********************************for debug***************************************/
+inline int Traverse_Total_Count_Table(Total_Count_Table* TCB)
+{
+    int i;
+    Count_Table* h;
+    khint_t k;
+
+    long long non_empty_k_mer = 0;
+
+    for (i = 0; i < TCB->size; i++)
+    {
+        h = TCB->sub_h[i];
+        for (k = kh_begin(h); k != kh_end(h); ++k)
+        {
+            if (kh_exist(h, k))            // test if a bucket contains data
+            {
+                non_empty_k_mer++;
+
+                if (kh_value(h, k)!= 0)
+                {
+                    fprintf(stderr, "ERROR when Traversing!\n");
+                }
+            }
+        }
+    }
+    
+    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);
+void destory_Total_Count_Table(Total_Count_Table* TCB);
+
+void init_Count_Table(Count_Table** table);
+
+/********************************for debug***************************************/
+void test_COUNT64();
+/********************************for debug***************************************/
+
+#endif