Merge pull request #31 from tseemann/max_filename_std

Use stdio FILENAME_MAX for path char[] sizes

Author: andrewjpage

src/fasta-of-snp-sites.c

@@ -31,8 +31,8 @@ void create_fasta_of_snp_sites(char filename[], int number_of_snps, char ** base
 	int snp_counter; 
 	char * base_filename;
 
-	base_filename = (char *) calloc(MAX_FILENAME_SIZE,sizeof(char));
-	memcpy(base_filename, filename, MAX_FILENAME_SIZE*sizeof(char));
+	base_filename = (char *) calloc(FILENAME_MAX,sizeof(char));
+	memcpy(base_filename, filename, FILENAME_MAX*sizeof(char));
 	fasta_file_pointer = fopen(base_filename, "w");
 
 	for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)

src/fasta-of-snp-sites.h

@@ -21,6 +21,8 @@
 #ifndef _FASTA_OF_SNP_SITES_
 #define _FASTA_OF_SNP_SITES_
 
+#include <stdio.h>
+
 void create_fasta_of_snp_sites(char filename[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples);
-#define MAX_FILENAME_SIZE 250
+
 #endif

src/main.c

@@ -26,8 +26,6 @@
 #include "snp-sites.h"
 #include "string-cat.h"
 
-#define MAX_FILENAME_SIZE 250
-
 static void print_usage()
 {
 	printf("Usage: snp_sites [-mvph] [-o output_filename] <file>\n");
@@ -41,8 +39,8 @@ static void print_usage()
 }
 
 int main (int argc, char **argv) {
-	char multi_fasta_filename[MAX_FILENAME_SIZE] = {""};
-	char output_filename[MAX_FILENAME_SIZE] = {""};
+	char multi_fasta_filename[FILENAME_MAX] = {""};
+	char output_filename[FILENAME_MAX] = {""};
 
 	int c;
 	int index;

src/phylib-of-snp-sites.c

@@ -32,8 +32,8 @@ void create_phylib_of_snp_sites(char filename[], int number_of_snps, char ** bas
 	int snp_counter;
 	char * base_filename;
 
-	base_filename = (char *) calloc(MAX_FILENAME_SIZE,sizeof(char));
-	memcpy(base_filename, filename, MAX_FILENAME_SIZE*sizeof(char));
+	base_filename = (char *) calloc(FILENAME_MAX,sizeof(char));
+	memcpy(base_filename, filename, FILENAME_MAX*sizeof(char));
 	fasta_file_pointer = fopen(base_filename, "w");
 
 	fprintf( fasta_file_pointer, "%d %d\n", number_of_samples, number_of_snps);

src/phylib-of-snp-sites.h

@@ -22,6 +22,8 @@
 #ifndef _PHYLIB_OF_SNP_SITES_
 #define _PHYLIB_OF_SNP_SITES_
 
+#include <stdio.h>
+
 void create_phylib_of_snp_sites(char filename[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples);
-#define MAX_FILENAME_SIZE 250
+
 #endif

src/snp-sites.c

@@ -87,8 +87,8 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
 
 	get_bases_for_each_snp(filename, snp_locations, bases_for_snps, length_of_genome, number_of_snps);
 
-	char output_filename_base[MAX_FILENAME_SIZE];
-	char filename_without_directory[MAX_FILENAME_SIZE];
+	char output_filename_base[FILENAME_MAX];
+	char filename_without_directory[FILENAME_MAX];
 	strip_directory_from_filename(filename, filename_without_directory);
 	memcpy(output_filename_base,filename_without_directory, size_of_string(filename_without_directory)+1 );
 
@@ -100,8 +100,8 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
 	if(output_vcf_file)
 	{
 		char * vcf_output_filename;
-		vcf_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
-		memcpy(vcf_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
+		vcf_output_filename = calloc(FILENAME_MAX,sizeof(char));
+		memcpy(vcf_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
 			char extension[5] = {".vcf"};
@@ -115,8 +115,8 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
   if(output_phylip_file)
   {
 		char *phylip_output_filename;
-		phylip_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
-		memcpy(phylip_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
+		phylip_output_filename = calloc(FILENAME_MAX,sizeof(char));
+		memcpy(phylip_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
 			char extension[10] = {".phylip"};
@@ -129,8 +129,8 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
   if((output_multi_fasta_file) || (output_vcf_file ==0 && output_phylip_file == 0 && output_multi_fasta_file == 0))
   {
 		char *multi_fasta_output_filename;
-		multi_fasta_output_filename = calloc(MAX_FILENAME_SIZE,sizeof(char));
-		memcpy(multi_fasta_output_filename, output_filename_base, (MAX_FILENAME_SIZE)*sizeof(char));
+		multi_fasta_output_filename = calloc(FILENAME_MAX,sizeof(char));
+		memcpy(multi_fasta_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
 			char extension[20] = {".snp_sites.aln"};
@@ -161,7 +161,7 @@ void strip_directory_from_filename(char * input_filename, char * output_filename
   int i;
   int end_index = 0;
   int last_forward_slash_index = -1;
-  for(i = 0; i< MAX_FILENAME_SIZE; i++)
+  for(i = 0; i< FILENAME_MAX; i++)
   {
     if(input_filename[i] == '/')
     {

src/snp-sites.h

@@ -21,13 +21,14 @@
 #ifndef _SNP_SITES_H_
 #define _SNP_SITES_H_
 
+#include <stdio.h>
+
 void build_snp_locations(int snp_locations[], char reference_sequence[]);
 int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_vcf_file, int output_phylip_file, char output_filename[]);
 int refilter_existing_snps(char * reference_bases, int number_of_snps, char ** column_names, int number_of_columns,int * snp_locations, int * filtered_snp_locations);
 void remove_filtered_snp_locations(int * filtered_snp_locations, int * snp_locations, int number_of_snps);
 void strip_directory_from_filename(char * input_filename, char * output_filename);
 
-#define MAX_FILENAME_SIZE 250
 #define MAX_SAMPLE_NAME_SIZE 1024
 
 #endif

src/vcf.c

@@ -32,7 +32,7 @@ void create_vcf_file(char filename[], int snp_locations[],int number_of_snps, ch
 {
 	FILE *vcf_file_pointer;
 	char * base_filename;
-	base_filename = (char *) malloc(MAX_FILENAME_SIZE*sizeof(char));
+	base_filename = (char *) malloc(FILENAME_MAX*sizeof(char));
 	strcpy(base_filename, filename);
 
 	vcf_file_pointer=fopen(base_filename, "w");

src/vcf.h

@@ -21,6 +21,8 @@
 #ifndef _VCF_H_
 #define _VCF_H_
 
+#include <stdio.h>
+
 void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int number_of_samples, size_t length_of_genome);
 void create_vcf_file(char filename[], int snp_locations[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples, size_t length_of_genome);
 void output_vcf_snps(FILE * vcf_file_pointer, char ** bases_for_snps, int * snp_locations, int number_of_snps, int number_of_samples);
@@ -30,7 +32,7 @@ char * alternative_bases(char reference_base, char * bases_for_snp, int number_o
 char * format_alternative_bases(char *);
 char * format_allele_index(char, char, char *);
 int check_if_char_in_string(char search_string[], char target_char, int search_string_length);
-#define MAX_FILENAME_SIZE 250
+
 #define MAXIMUM_NUMBER_OF_ALT_BASES 30
 
 #endif