diff --git a/src/alignment_file.c b/src/alignment_file.c
index 6b60062d..afc64a40 100644
--- a/src/alignment_file.c
+++ b/src/alignment_file.c
@@ -218,31 +218,6 @@ int detect_snps(char reference_sequence[], char filename[], int length_of_genome
 
 
 
-int read_first_few_characters_of_line(char sequence[], FILE * pFilePtr, int max_characters)
-{
-    
-    char *pcRes         = NULL;  
-    int   lineLength    = 0; 
-	char current_line_buffer[MAX_READ_BUFFER_SMALL] = {0};
-	
-	
-    while((pcRes = fgets(current_line_buffer, MAX_READ_BUFFER_SMALL, pFilePtr))  != NULL){
-	      if(lineLength < max_characters)
-      	{
-          //append string to line buffer
-          strcat(sequence, current_line_buffer);
-          strcpy(current_line_buffer, "");
-          lineLength = strlen(sequence) - 1;
-          //if end of line character is found then exit from loop
-	        if((sequence)[lineLength] == '\n' || (sequence)[lineLength] == '\0'){
-	            break;
-	        }
-        }
-    }
-    return 1;
-}
-
-
 
 char * read_line(char sequence[], FILE * pFilePtr)
 {
diff --git a/src/alignment_file.h b/src/alignment_file.h
index 567f9e4b..0eb24c29 100644
--- a/src/alignment_file.h
+++ b/src/alignment_file.h
@@ -33,8 +33,6 @@ 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 65536
 #define MAX_READ_BUFFER_SMALL 1024
diff --git a/src/parse_vcf.c b/src/parse_vcf.c
index 97f1c03e..ddc4fcc5 100644
--- a/src/parse_vcf.c
+++ b/src/parse_vcf.c
@@ -32,14 +32,15 @@ int * column_data;
 void get_integers_from_column_in_vcf(FILE * vcf_file_pointer, int * integer_values, int number_of_snps, int column_number)
 {
 	rewind(vcf_file_pointer);
-	char szBuffer[100000] = {0};  
+	char * szBuffer;
+	szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
 	int reference_index = 0;
 	char result[1000] = {0};  
 	
 	do{
 		strcpy(szBuffer,""); 
-		// check the first character of the line to see if its in the header
-		read_first_few_characters_of_line(szBuffer, vcf_file_pointer, 50);
+ 		// check the first character of the line to see if its in the header
+  	szBuffer = read_line(szBuffer, vcf_file_pointer);
 		
 		if(szBuffer[0] == '\0')
 		{
@@ -61,14 +62,15 @@ void get_integers_from_column_in_vcf(FILE * vcf_file_pointer, int * integer_valu
 void get_sequence_from_column_in_vcf(FILE * vcf_file_pointer, char * sequence_bases, int number_of_snps, int column_number)
 {
 	rewind(vcf_file_pointer);
-	char szBuffer[10000] = {0};  
+	char * szBuffer;
+	szBuffer = (char *) malloc(MAX_READ_BUFFER*sizeof(char));
 	int reference_index = 0;
 	char result[1000] = {0};  
 		
 	do{
 		strcpy(szBuffer,""); 
 		// check the first character of the line to see if its in the header
-		read_first_few_characters_of_line(szBuffer, vcf_file_pointer, 1000);
+		szBuffer = read_line(szBuffer, vcf_file_pointer);
 		
 		if(szBuffer[0] == '\0')
 		{