Merge pull request #35 from andrewjpage/master

resize read line buffer
nickjcroucher · Jun 11, 2012 · 6646d3f · 6646d3f
2 parents 17ec31b + ed1db06
commit 6646d3f
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Showing 6 changed files with 16 additions and 8 deletions.
diff --git a/src/alignment_file.c b/src/alignment_file.c
@@ -253,7 +253,11 @@ int read_line(char sequence[], FILE * pFilePtr)
 
 
     while((pcRes = fgets(current_line_buffer, sizeof(current_line_buffer), pFilePtr))  != NULL){
-        //append string to line buffer
+        if( strlen(current_line_buffer) > MAX_READ_BUFFER - 10 )
+        {
+					realloc(sequence, strlen(sequence) + MAX_READ_BUFFER + 10 );
+	      }
+
         strcat(sequence, current_line_buffer);
         strcpy(current_line_buffer, "");
         lineLength = strlen(sequence) - 1;

diff --git a/src/alignment_file.h b/src/alignment_file.h
@@ -36,7 +36,7 @@ void get_bases_for_each_snp(char filename[], int snp_locations[], char ** bases_
 int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_characters);
 
 
-#define MAX_READ_BUFFER 1048576
+#define MAX_READ_BUFFER 262144
 #define MAX_READ_BUFFER_SMALL 1024
 #define MAX_SAMPLE_NAME_SIZE 1024
 

diff --git a/src/parse_phylip.c b/src/parse_phylip.c
@@ -260,7 +260,9 @@ int number_of_snps_in_phylib()
 void load_sequences_from_phylib(FILE * phylip_file_pointer)
 {	
 	rewind(phylip_file_pointer);
-	char line_buffer[MAX_READ_BUFFER] = {0}; 
+	char * line_buffer;
+	line_buffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
+
 	int i;
 
 	// The first line contains the number of samples and snps

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 1048576
+#define MAX_READ_BUFFER 262144
 #define MAX_SAMPLE_NAME_SIZE 1024
 
 

diff --git a/src/parse_vcf.c b/src/parse_vcf.c
@@ -167,14 +167,15 @@ int get_number_of_columns(char * column_header)
 int get_number_of_columns_from_file(FILE * vcf_file_pointer)
 {
 	rewind(vcf_file_pointer);
-	char szBuffer[100000] = {0};
 	char result[100] = {0};
 
+	char * szBuffer;
+	szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
+
 	do{
 		strcpy(szBuffer,""); 
 		// check the first character of the line to see if its in the header
 		read_line(szBuffer, vcf_file_pointer);
-
 		if(szBuffer[0] == '\0' || szBuffer[0] != '#')
 		{
 			break;
@@ -195,7 +196,8 @@ int get_number_of_columns_from_file(FILE * vcf_file_pointer)
 void get_column_names(FILE * vcf_file_pointer, char ** column_names, int number_of_columns)
 {
 	rewind(vcf_file_pointer);
-	char szBuffer[100000] = {0};
+	char * szBuffer;
+	szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
 	char result[100] = {0};  
 	int i;
 

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
 
 #endif