Merge pull request #37 from andrewjpage/read_line_memory_leak

Read line memory leak
nickjcroucher · Jun 12, 2012 · 8f983f7 · 8f983f7
2 parents 6646d3f + da27ac7
commit 8f983f7
Show file tree

Hide file tree

Showing 6 changed files with 23 additions and 18 deletions.
diff --git a/src/alignment_file.c b/src/alignment_file.c
@@ -244,20 +244,19 @@ int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_
 
 
 
-int read_line(char sequence[], FILE * pFilePtr)
+char * read_line(char sequence[], FILE * pFilePtr)
 {
-
+    strcpy(sequence, "");
     char *pcRes         = NULL;  
-    int   lineLength    = 0; 
+    long   lineLength    = 0; 
 	char current_line_buffer[MAX_READ_BUFFER] = {0};
 
 
     while((pcRes = fgets(current_line_buffer, sizeof(current_line_buffer), pFilePtr))  != NULL){
-        if( strlen(current_line_buffer) > MAX_READ_BUFFER - 10 )
-        {
-					realloc(sequence, strlen(sequence) + MAX_READ_BUFFER + 10 );
-	      }
-
+	      if(strlen(sequence) > 0)
+	      {
+	    			sequence = realloc(sequence, strlen(sequence) + strlen(current_line_buffer) + 2 );
+        }
         strcat(sequence, current_line_buffer);
         strcpy(current_line_buffer, "");
         lineLength = strlen(sequence) - 1;
@@ -269,7 +268,7 @@ int read_line(char sequence[], FILE * pFilePtr)
     }
 
 
-    return 1;
+    return sequence;
 }
 
 

diff --git a/src/alignment_file.h b/src/alignment_file.h
@@ -28,15 +28,15 @@ int build_reference_sequence(char reference_sequence[], char filename[]);
 void advance_to_sequence(FILE * alignment_file_pointer);
 void advance_to_sequence_name(FILE * alignment_file_pointer);
 int genome_length(char filename[]);
-int read_line(char sequence[], FILE * pFilePtr);
+char * read_line(char sequence[], FILE * pFilePtr);
 int number_of_sequences_in_file(char filename[]);
 void get_sample_names_for_header(char filename[], char ** sequence_names, int number_of_samples);
 char filter_invalid_characters(char input_char);
 void get_bases_for_each_snp(char filename[], int snp_locations[], char ** bases_for_snps, int length_of_genome, int number_of_snps);
 int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_characters);
 
 
-#define MAX_READ_BUFFER 262144
+#define MAX_READ_BUFFER 65536
 #define MAX_READ_BUFFER_SMALL 1024
 #define MAX_SAMPLE_NAME_SIZE 1024
 

diff --git a/src/parse_phylip.c b/src/parse_phylip.c
@@ -267,7 +267,7 @@ void load_sequences_from_phylib(FILE * phylip_file_pointer)
 
 	// The first line contains the number of samples and snps
 	strcpy(line_buffer,"");
-	read_line(line_buffer, phylip_file_pointer);
+	line_buffer = read_line(line_buffer, phylip_file_pointer);
 
 	num_samples = get_number_of_samples_from_phylip(line_buffer);
 	num_snps = get_number_of_snps_from_phylip(line_buffer);
@@ -286,7 +286,10 @@ void load_sequences_from_phylib(FILE * phylip_file_pointer)
 
 	do{
 		strcpy(line_buffer,""); 
-		read_line(line_buffer, phylip_file_pointer);
+		free(line_buffer);
+		line_buffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
+
+		line_buffer = read_line(line_buffer, phylip_file_pointer);
 
 		if(line_buffer[0] == '\0')
 		{
@@ -325,7 +328,7 @@ void load_sequences_from_phylib(FILE * phylip_file_pointer)
 		sample_counter++;
 
 	}while(line_buffer[0] != '\0');
-
+	free(line_buffer);
 	initialise_statistics();
 }
 

diff --git a/src/parse_phylip.h b/src/parse_phylip.h
@@ -49,7 +49,7 @@ void set_number_of_blocks_for_sample(char * sample_name,int num_blocks);
 sample_statistics ** get_sample_statistics();
 int number_of_snps_in_phylib();
 
-#define MAX_READ_BUFFER 262144
+#define MAX_READ_BUFFER 65536
 #define MAX_SAMPLE_NAME_SIZE 1024
 
 

diff --git a/src/parse_vcf.c b/src/parse_vcf.c
@@ -175,7 +175,7 @@ int get_number_of_columns_from_file(FILE * vcf_file_pointer)
 	do{
 		strcpy(szBuffer,""); 
 		// check the first character of the line to see if its in the header
-		read_line(szBuffer, vcf_file_pointer);
+		szBuffer = read_line(szBuffer, vcf_file_pointer);
 		if(szBuffer[0] == '\0' || szBuffer[0] != '#')
 		{
 			break;
@@ -204,7 +204,9 @@ void get_column_names(FILE * vcf_file_pointer, char ** column_names, int number_
 	do{
 		strcpy(szBuffer,""); 
 		// check the first character of the line to see if its in the header
-		read_line(szBuffer, vcf_file_pointer);
+		free(szBuffer);
+		szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
+		szBuffer = read_line(szBuffer, vcf_file_pointer);
 
 		if(szBuffer[0] == '\0' || szBuffer[0] != '#')
 		{
@@ -223,6 +225,7 @@ void get_column_names(FILE * vcf_file_pointer, char ** column_names, int number_
 		}
 
 	}while(szBuffer[0] != '\0');
+	free(szBuffer);
 }
 
 // Assume the sample names are unique

diff --git a/src/parse_vcf.h b/src/parse_vcf.h
@@ -31,6 +31,6 @@ void get_column_names(FILE * vcf_file_pointer, char ** column_names, int number_
 int column_number_for_column_name(char ** column_names, char * column_name, int number_of_columns);
 
 void get_integers_from_column_in_vcf(FILE * vcf_file_pointer, int * integer_values, int number_of_snps, int column_number);
-#define MAX_READ_BUFFER 262144
+#define MAX_READ_BUFFER 65536
 
 #endif