revert to 1.0.1.6

chhylp123 · Aug 23, 2019 · d6218af · d6218af
1 parent 6f23aa4
commit d6218af
Show file tree

Hide file tree

Showing 17 changed files with 3,378 additions and 7,832 deletions.
diff --git a/Auxiliary.h b/Auxiliary.h
@@ -22,7 +22,7 @@ extern unsigned char    default_ws;
 extern unsigned char	MERGE_STEP;
 extern unsigned short	SEQ_LENGTH;		// Sequence(read) length
 
-extern char				*versionN;
+extern char				*versionN;
 
 
 extern unsigned int		THREAD_COUNT;
@@ -71,19 +71,6 @@ extern int unmapped_out;
 extern int ambiguous_out;
 extern int mapstats;
 
-
-extern int GapOpenPenalty;
-extern int GapExtensionPenalty;
-extern int MistMatchPenaltyMax;
-extern int MistMatchPenaltyMin;
-extern int N_Penalty;
-extern int Q_base;
-
-extern char *Mapstats_File;
-extern char *Mapstats_File_Path;
-
-
-
 double	Get_T(void);
 void	reverseComplement (char *seq, char *rcSeq , int length);
 ///void    reverse_pattern(char* pattern, char* rev_pattern, int length);

diff --git a/Bitmapper_main.cpp b/Bitmapper_main.cpp
@@ -45,11 +45,6 @@ int main(int argc, char *argv[])
     {
 
 
-	  fprintf(stderr,"Read qualities are encoded by Phred+%d...\n", Q_base);
-	  fprintf(stderr,"GapOpenPenalty: %d, GapExtensionPenalty: %d, MistMatchPenaltyMax: %d\n", 
-	  GapOpenPenalty, GapExtensionPenalty, MistMatchPenaltyMax);
-	  fprintf(stderr,"MistMatchPenaltyMin: %d, N_Penalty: %d\n", 
-	  MistMatchPenaltyMin, N_Penalty);
 
 
       double totalLoadingTime = 0;
@@ -58,7 +53,6 @@ int main(int argc, char *argv[])
       double loadingTime;
       double mappingTime;
       char outputFileName[NAME_LENGTH];
-	  char bam_outputFileName[NAME_LENGTH];
 
 
 
@@ -74,7 +68,6 @@ int main(int argc, char *argv[])
          return 1;
       }
 
-<<<<<<< HEAD
 	  if(Mapped_File)
 	  {
 		  sprintf(outputFileName, "%s%s",Mapped_FilePath , Mapped_File);
@@ -84,21 +77,8 @@ int main(int argc, char *argv[])
 		  outputFileName[0] = '\0';
 	  }
 
-
-=======
-
-	  sprintf(outputFileName, "%s%s",Mapped_FilePath , Mapped_File);
-	  sprintf(bam_outputFileName, "%s.tmp", outputFileName);
-
-
 
-	   if (output_methy == 0)
-	   {
-			Output_gene(outputFileName);   
-	   }
-
-
->>>>>>> parent of e8092b5... improve output
+
 
         if (!is_pairedEnd)
         {
@@ -113,8 +93,6 @@ int main(int argc, char *argv[])
             mappingTime = 0;
             loadingTime = 0;
 
-
-
             fprintf(stderr,"Start load hash table!\n");
 
 			Load_Index(thread_e, &chhy_ih_refGenName, &refChromeCont, fileName[1]);
@@ -125,14 +103,16 @@ int main(int argc, char *argv[])
 
 			if (output_methy == 0)
 			{
-				//这个Prepare_alignment()就是将这个文件里的变量各种配置到新文件中
-				OutPutSAM_Nounheader(chhy_ih_refGenName, refChromeCont, argc, argv);
-
-
-				if (bam_output == 1)
+				if (bam_output == 0)
+				{
+					Output_gene(outputFileName);   
+					OutPutSAM_Nounheader(chhy_ih_refGenName, refChromeCont, argc, argv);
+				}
+				else
 				{
-					init_bam_file_from_sam(outputFileName, bam_outputFileName);
+					init_bam_header(outputFileName, chhy_ih_refGenName, refChromeCont, argc, argv);
 				}
+
 			}
 
 
@@ -147,12 +127,15 @@ int main(int argc, char *argv[])
 				if (pbat == 0)
 				{
 					Map_Single_Seq(0);
+
 					///Map_Single_Seq_end_to_end_cover(0);
+
 				}
 				else
 				{
 					Map_Single_Seq_pbat(0);
 				}
+
 			}
             else
             {
@@ -217,30 +200,32 @@ int main(int argc, char *argv[])
 				fprintf(stderr, "Start alignment in sensitive mode.\n");
 			}
 
-
-			///fprintf(stderr, "is_local: %d\n", is_local);
 
 
 			if (output_methy == 0)
 			{
-
-				OutPutSAM_Nounheader(chhy_ih_refGenName, refChromeCont, argc, argv);
-
-				if (bam_output == 1)
+				if (bam_output == 0)
 				{
-					init_bam_file_from_sam(outputFileName, bam_outputFileName);
+					Output_gene(outputFileName); 
+					OutPutSAM_Nounheader(chhy_ih_refGenName, refChromeCont, argc, argv);
 				}
+				else
+				{
+					init_bam_header(outputFileName, chhy_ih_refGenName, refChromeCont, argc, argv);
+				}
+
 			}
 
 
             startTime = Get_T();
 
 			Prepare_alignment(outputFileName, fileName[0], chhy_ih_refGenName, refChromeCont, read_format, is_pairedEnd);
 
+
              if(THREAD_COUNT==1)
             {
 
-				 Map_Pair_Seq(0);
+				Map_Pair_Seq(0);
             }
             else
             {
@@ -263,9 +248,7 @@ int main(int argc, char *argv[])
 
 		if (bam_output == 1)
 		{
-			///close_bam_file();
-			close_bam_file_rename(bam_outputFileName, outputFileName);
-
+			close_bam_file();
 		}
 
 	  ///这个一打开速度就奇慢，不知道为什么
@@ -298,18 +281,19 @@ int main(int argc, char *argv[])
 
 	  if (mapstats == 1)
 	  {
-<<<<<<< HEAD
-		  sprintf(Mapstats_File_Path + strlen(Mapstats_File_Path), "%s", Mapstats_File);
-		  fprintf(stderr, "The statistical information will be written to %s ...\n", Mapstats_File_Path);
-
-		  FILE* mapstats_fp = fopen(Mapstats_File_Path, "w");
-=======
 		  char mapstatsFileName[NAME_LENGTH];
 
-		  sprintf(mapstatsFileName, "%s.mapstats", outputFileName);
-
+		  if (outputFileName[0] == '\0')
+		  {
+			  sprintf(mapstatsFileName, "stdout.mapstats");
+		  }
+		  else
+		  {
+			  sprintf(mapstatsFileName, "%s.mapstats", outputFileName);
+		  }
+
+
 		  FILE* mapstats_fp = fopen(mapstatsFileName, "w");
->>>>>>> parent of e8092b5... improve output
 
 		  if (mapstats_fp != NULL)
 		  {