Fix bug

Assembly.cpp

@@ -400,18 +400,29 @@ void Build_hash_table_multiple_thr()
     {
         write_Total_Pos_Table(&PCB, read_file_name);
         destory_Total_Pos_Table(&PCB);
-        load_Total_Pos_Table(&PCB, read_file_name);
+        ///load_Total_Pos_Table(&PCB, read_file_name);
 
         write_All_reads(&R_INF, read_file_name);
         destory_All_reads(&R_INF);
-        load_All_reads(&R_INF, read_file_name);
+        ///load_All_reads(&R_INF, read_file_name);
     }
     
 
     
 }
 
+int load_pre_cauculated_index()
+{
+    if(load_Total_Pos_Table(&PCB, read_file_name) && load_All_reads(&R_INF, read_file_name))
+    {
+        return 1;
+    }
+    else
+    {
+        return 0;
+    }
     
+}
 
 
 /********************************for debug***************************************/
@@ -508,15 +519,18 @@ void verify_Position_hash_table()
     while (get_read(seq))
     {
 
+
         if (seq->seq.l
             != Get_READ_LENGTH(R_INF, read_number))
         {
             fprintf(stderr, "seq error\n");
         }
 
+
         recover_UC_Read(&g_read, &R_INF, read_number);
 
 
+
         if(memcmp(seq->seq.s, g_read.seq, seq->seq.l))
         {
             fprintf(stderr, "\nseq error ID: %llu, length: %llu\n",read_number, seq->seq.l);
@@ -536,7 +550,6 @@ void verify_Position_hash_table()
         }
 
 
-
         init_HPC_seq(&HPC_read, seq->seq.s, seq->seq.l);
         init_Hash_code(&k_code);
 
@@ -545,6 +558,8 @@ void verify_Position_hash_table()
 
         while ((code = get_HPC_code(&HPC_read)) != 6)
         {
+
+
             if(code < 4)
             {
                 k_mer_append(&k_code,code,k_mer_length);
@@ -552,13 +567,16 @@ void verify_Position_hash_table()
                 if (avalible_k>=k_mer_length)
                 {
 
-                    uint64_t count1 = get_Total_Count_Table(&TCB, &k_code, k_mer_length);
+                    ///uint64_t count1 = get_Total_Count_Table(&TCB, &k_code, k_mer_length);
                     uint64_t count2 = count_Total_Pos_Table(&PCB, &k_code, k_mer_length);
+                    /**
                     if(count1>=k_mer_min_freq && count1<= k_mer_max_freq && count1!=count2)
                     {
                         fprintf(stderr, "count1: %lld\n",count1);
                         fprintf(stderr, "count2: %lld\n",count2);
                     }
+                    **/
+
 
 
                     if(locate_Total_Pos_Table(&PCB, &k_code, &list, k_mer_length, &sub_ID) == count2)

Assembly.h

@@ -8,6 +8,7 @@
 
 void Counting_multiple_thr();
 void Build_hash_table_multiple_thr();
+int load_pre_cauculated_index();
 
 /********************************for debug***************************************/
 void Verify_Counting();

Hash_Table.cpp

@@ -131,12 +131,17 @@ void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
 }
 
 
-void load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
+int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
 {
     fprintf(stdout, "Loading index to disk ...... \n");
     char* index_name = (char*)malloc(strlen(read_file_name)+5);
     sprintf(index_name, "%s.idx", read_file_name);
     FILE* fp = fopen(index_name, "r");
+    if (!fp)
+    {
+        return 0;
+    }
+    
     
     fread(&TCB->prefix_bits, sizeof(TCB->prefix_bits), 1, fp);
     fread(&TCB->suffix_bits, sizeof(TCB->suffix_bits), 1, fp);
@@ -184,6 +189,7 @@ void load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name)
     fclose(fp);
     fprintf(stdout, "Index has been loaded.\n");
 
+    return 1;
 }
 
 

Hash_Table.h

@@ -294,7 +294,7 @@ void init_Count_Table(Count_Table** table);
 void init_Pos_Table(Count_Table** pre_table, Pos_Table** table);
 void destory_Total_Pos_Table(Total_Pos_Table* TCB);
 void write_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
-void load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
+int load_Total_Pos_Table(Total_Pos_Table* TCB, char* read_file_name);
 
 
 

Process_Read.cpp

@@ -107,12 +107,18 @@ void write_All_reads(All_reads* r, char* read_file_name)
 
 
 
-void load_All_reads(All_reads* r, char* read_file_name)
+int load_All_reads(All_reads* r, char* read_file_name)
 {
     fprintf(stdout, "Loading reads to disk ...... \n");
     char* index_name = (char*)malloc(strlen(read_file_name)+5);
     sprintf(index_name, "%s.bin", read_file_name);
     FILE* fp = fopen(index_name, "r");
+	if (!fp)
+    {
+        return 0;
+    }
+
+
     fread(&r->index_size, sizeof(r->index_size), 1, fp);
 	fread(&r->name_index_size, sizeof(r->name_index_size), 1, fp);
 	fread(&r->total_reads, sizeof(r->total_reads), 1, fp);
@@ -162,6 +168,8 @@ void load_All_reads(All_reads* r, char* read_file_name)
     free(index_name);    
     fclose(fp);
     fprintf(stdout, "Reads has been loaded.\n");
+
+	return 1;
 }
 
 

Process_Read.h

@@ -111,7 +111,7 @@ void init_UC_Read(UC_Read* r);
 void recover_UC_Read(UC_Read* r, All_reads* R_INF, uint64_t ID);
 void reverse_complement(char* pattern, uint64_t length);
 void write_All_reads(All_reads* r, char* read_file_name);
-void load_All_reads(All_reads* r, char* read_file_name);
+int load_All_reads(All_reads* r, char* read_file_name);
 void destory_All_reads(All_reads* r);
 
 void Counting_block();

main.cpp

@@ -21,20 +21,26 @@ int main(int argc, char *argv[])
     if (!CommandLine_process(argc, argv))
         return 1;
 
-    ///init_kseq(read_file_name);
 
     fprintf(stdout, "k-mer length: %d\n",k_mer_length);
 
-    ///Counting();
+    if (load_index_from_disk && load_pre_cauculated_index())
-    Counting_multiple_thr();
+    {
+        ;
+    }
+    else
+    {
+        Counting_multiple_thr();
+
+        Build_hash_table_multiple_thr();
+    }
+    
+
     
-    Build_hash_table_multiple_thr();
 
     ///verify_Position_hash_table();
 
-    ///destory_kseq();
 
-    ///debug_Counting();
 
 
     return 1;