Fix a minor bug when mapping

Bitmapper_main.cpp

@@ -35,10 +35,6 @@ int main(int argc, char *argv[])
 
   if (!CommandLine_process(argc, argv))
     return 1;
-
-
-
-  fprintf(stdout, "bam_output:%d\n", bam_output);
 
 
   if(is_index)
@@ -57,7 +53,7 @@ int main(int argc, char *argv[])
       double loadingTime;
       double mappingTime;
       char outputFileName[NAME_LENGTH];
-	  char bam_outputFileName[NAME_LENGTH];
+	  char bam_outputFileName[NAME_LENGTH];
 
 
 
@@ -69,52 +65,43 @@ int main(int argc, char *argv[])
 	  ///这就是打开read文件
 	  if (!initiReadAllReads(Read_File1, Read_File2, is_pairedEnd, &read_format))
       {
-		 fprintf(stdout, "Cannot open read files. \n");
+		 fprintf(stderr, "Cannot open read files. \n");
          return 1;
       }
 
 
+	  sprintf(outputFileName, "%s%s",Mapped_FilePath , Mapped_File);
+	  sprintf(bam_outputFileName, "%s.tmp", outputFileName);
 
-
-       sprintf(outputFileName, "%s%s",Mapped_FilePath , Mapped_File);
-	   sprintf(bam_outputFileName, "%s.tmp", outputFileName);
+
 
 	   if (output_methy == 0)
 	   {
-
-
-			Output_gene(outputFileName);
-
+			Output_gene(outputFileName);   
 	   }
 
 
 
         if (!is_pairedEnd)
         {
 
-          if (!Start_Load_Index(fileName[1]))
-            {
-            fprintf(stderr, "Load hash table index failed!\n");
-            return 1;
-            }
+          	if (!Start_Load_Index(fileName[1]))
+			{
+				fprintf(stderr, "Load hash table index failed!\n");
+				return 1;
+			}
 
 
             mappingTime = 0;
             loadingTime = 0;
-             //loadHashTable = &Load_Index;
-            fprintf(stdout,"Start load hash table!\n");
-
-
-			///fprintf(stdout, "%d\n", READS_QUENUE_MAX_LENGTH);
-
-			fprintf(stderr, "%s\n", fileName[1]);
 
-             // loadHashTable = &Load_Index;
+            fprintf(stderr,"Start load hash table!\n");
+
 			Load_Index(thread_e, &chhy_ih_refGenName, &refChromeCont, fileName[1]);
 
 
             totalLoadingTime += Get_T()-startTime;
-            fprintf(stdout, "Start alignment!\n");
+            fprintf(stderr, "Start alignment!\n");
 
 			if (output_methy == 0)
 			{
@@ -162,17 +149,16 @@ int main(int argc, char *argv[])
 				}
             }
 
-
+
             totalMappingTime += Get_T()-startTime;
-            fprintf(stdout, "sucess!\n");
 
         }
         else
         {
-			if (output_methy == 1 && methylation_size % 2 != 0)
-			{
-				fprintf(stdout, "The variable 'methylation_size' must be an even! Please change it to be even!\n");
-				exit(1);
+			if (output_methy == 1 && methylation_size % 2 != 0)
+			{
+				fprintf(stderr, "The variable 'methylation_size' must be an even! Please change it to be even!\n");
+				exit(1);
 			}
 
 			///_r_fp1
@@ -195,7 +181,7 @@ int main(int argc, char *argv[])
             mappingTime = 0;
             loadingTime = 0;
              //loadHashTable = &Load_Index;
-             fprintf(stdout,"Start load hash table!\n");
+             fprintf(stderr,"Start load hash table!\n");
              // loadHashTable = &Load_Index;
 			 Load_Index(thread_e, &chhy_ih_refGenName, &refChromeCont, fileName[1]);
 
@@ -207,11 +193,11 @@ int main(int argc, char *argv[])
 
 			if (is_local == 1)
 			{
-				fprintf(stdout, "Start alignment in default fast mode.\n");
+				fprintf(stderr, "Start alignment in default fast mode.\n");
 			}
 			else
 			{
-				fprintf(stdout, "Start alignment in sensitive mode.\n");
+				fprintf(stderr, "Start alignment in sensitive mode.\n");
 			}
 
 
@@ -241,8 +227,8 @@ int main(int argc, char *argv[])
 				 Map_Pair_Seq(0);
             }
             else
-            {
-				Map_Pair_Seq_muti_thread(0);
+            {
+				Map_Pair_Seq_muti_thread(0);
 
             }
 
@@ -255,25 +241,24 @@ int main(int argc, char *argv[])
 
 
             totalMappingTime += Get_T()-startTime;
-            fprintf(stdout, "sucess!\n");
 
         }
 
 
 		if (bam_output == 1)
 		{
 			///close_bam_file();
-			close_bam_file_rename(bam_outputFileName, outputFileName);
+			close_bam_file_rename(bam_outputFileName, outputFileName);
 
 		}
 
 	  ///这个一打开速度就奇慢，不知道为什么
       ///finalizeOutput();
 
-      fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
-      fprintf(stdout, "%19s%16.2f%18.2f\n\n", "Total:",totalLoadingTime, totalMappingTime);
+      fprintf(stderr, "-----------------------------------------------------------------------------------------------------------\n");
+      fprintf(stderr, "%19s%16.2f%18.2f\n\n", "Total:",totalLoadingTime, totalMappingTime);
 
-      fprintf(stdout, "%-42s%10.2f\n","Total Time:", totalMappingTime+totalLoadingTime);
+      fprintf(stderr, "%-42s%10.2f\n","Total Time:", totalMappingTime+totalLoadingTime);
 
 	  long long number_of_read;
 	  long long number_of_unique_mapped_read;
@@ -284,15 +269,15 @@ int main(int argc, char *argv[])
 	  get_mapping_informations(&number_of_read, &number_of_unique_mapped_read, &number_of_ambiguous_mapped_read,
 		  &number_of_unmapped_read, &number_of_mapped_bases, &number_of_mapped_errors);
 
-	  fprintf(stdout, "%-48s%lld\n", "No. of Reads:", number_of_read);
-	  fprintf(stdout, "%-48s%lld (%0.2f\%)\n", "No. of Unique Mapped Reads:", 
+	  fprintf(stderr, "%-48s%lld\n", "No. of Reads:", number_of_read);
+	  fprintf(stderr, "%-48s%lld (%0.2f\%)\n", "No. of Unique Mapped Reads:", 
 		  number_of_unique_mapped_read, ((double)number_of_unique_mapped_read / (double)number_of_read)*100);
-	  fprintf(stdout, "%-48s%lld (%0.2f\%)\n", "No. of Ambiguous Mapped Reads:", 
+	  fprintf(stderr, "%-48s%lld (%0.2f\%)\n", "No. of Ambiguous Mapped Reads:", 
 		  number_of_ambiguous_mapped_read, ((double)number_of_ambiguous_mapped_read / (double)number_of_read) * 100);
-	  fprintf(stdout, "%-48s%lld (%0.2f\%)\n", "No. of Unmapped Reads:", 
+	  fprintf(stderr, "%-48s%lld (%0.2f\%)\n", "No. of Unmapped Reads:", 
 		  number_of_unmapped_read, ((double)number_of_unmapped_read / (double)number_of_read) * 100);
 
-	  fprintf(stdout, "%-47s %0.2f\%\n", "Mismatch and Indel Rate:",
+	  fprintf(stderr, "%-47s %0.2f\%\n", "Mismatch and Indel Rate:",
 		  ((double)number_of_mapped_errors / (double)number_of_mapped_bases) * 100);
 
 	  if (mapstats == 1)
@@ -327,8 +312,8 @@ int main(int argc, char *argv[])
 		double total_time = 0;
 		double startTime = Get_T();
 
-		fprintf(stdout, "minVariantDepth: %d\n", minVariantDepth);
-		fprintf(stdout, "maxVariantFrac: %f\n", maxVariantFrac);
+		fprintf(stderr, "minVariantDepth: %d\n", minVariantDepth);
+		fprintf(stderr, "maxVariantFrac: %f\n", maxVariantFrac);
 
 		sprintf(fileName[1], "%s.methy", fileName[1]);
 
@@ -349,8 +334,8 @@ int main(int argc, char *argv[])
 
 		get_genome_cuts(Read_File1);
 
-		fprintf(stdout, "genome_cuts: %d\n", genome_cuts);
-		fprintf(stdout, "PE_distance: %d\n", maxDistance_pair);
+		fprintf(stderr, "genome_cuts: %d\n", genome_cuts);
+		fprintf(stderr, "PE_distance: %d\n", maxDistance_pair);
 
 		init_output_methy(Read_File1, need_context);
 
@@ -364,7 +349,7 @@ int main(int argc, char *argv[])
 		if (!is_pairedEnd)
 		{
 
-			fprintf(stdout, "Extract from single-end alignment ...\n");
+			fprintf(stderr, "Extract from single-end alignment ...\n");
 
 			if (THREAD_COUNT == 1)
 			{
@@ -377,7 +362,7 @@ int main(int argc, char *argv[])
 		}
 		else
 		{
-			fprintf(stdout, "Extract from paired-end alignment ...\n");
+			fprintf(stderr, "Extract from paired-end alignment ...\n");
 
 			if (THREAD_COUNT == 1)
 			{
@@ -393,8 +378,8 @@ int main(int argc, char *argv[])
 
 		total_time += Get_T() - startTime;
 
-		fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
-		fprintf(stdout, "%19s%16.2f\n\n", "Total:", total_time);
+		fprintf(stderr, "-----------------------------------------------------------------------------------------------------------\n");
+		fprintf(stderr, "%19s%16.2f\n\n", "Total:", total_time);
 	}