Major cleanup to use standard C string functions

README.md

@@ -10,6 +10,7 @@ This program finds snp sites from a multi fasta alignment file.
  -p		    output a phylip file
  -o		    specify an output filename
  -h		    this help message
+ -V		    print version and exit
  <file>		input alignment file which can optionally be gzipped
 ```
 

snp-sites.txt

@@ -34,6 +34,9 @@ OPTIONS
 *-h*::
 	This document
 
+*-V*::
+	Show version and exit
+
 EXAMPLES
 --------
 snp-sites my-alignment.aln

src/alignment-file.c

@@ -226,13 +226,13 @@ char * read_line(char sequence[], FILE * pFilePtr)
 
 
   while((pcRes = fgets(current_line_buffer, sizeof(current_line_buffer), pFilePtr))  != NULL){
-    if(size_of_string(sequence) > 0)
+    if(strlen(sequence) > 0)
       {
-	sequence = realloc(sequence, sizeof(char)*(size_of_string(sequence) + size_of_string(current_line_buffer) + 2) );
+	sequence = realloc(sequence, sizeof(char)*(strlen(sequence) + strlen(current_line_buffer) + 2) );
       }
-    concat_strings_created_with_malloc(sequence,current_line_buffer);
+    strcat(sequence,current_line_buffer);
     current_line_buffer[0] = '\0';
-    lineLength = size_of_string(sequence);
+    lineLength = strlen(sequence);
     //if end of line character is found then exit from loop
 
     if((sequence)[lineLength] == '\n' || (sequence)[lineLength] == '\0'){
@@ -257,7 +257,7 @@ void get_sample_names_for_header(char filename[], char ** sequence_names, int nu
 	seq = kseq_init(fp);
 
 	while ((l = kseq_read(seq)) >= 0) {
-		memcpy(sequence_names[i], seq->name.s, size_of_string(seq->name.s)+1);
+		strcpy(sequence_names[i], seq->name.s);
     i++;
 	}
 	kseq_destroy(seq);

src/fasta-of-snp-sites.c

@@ -29,21 +29,17 @@ void create_fasta_of_snp_sites(char filename[], int number_of_snps, char ** base
 	FILE *fasta_file_pointer;
 	int sample_counter;
 	int snp_counter; 
-	char * base_filename;
-
-	base_filename = (char *) calloc(FILENAME_MAX,sizeof(char));
-	memcpy(base_filename, filename, FILENAME_MAX*sizeof(char));
-	fasta_file_pointer = fopen(base_filename, "w");
+
+	fasta_file_pointer = fopen(filename, "w");
 
 	for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
 	{
 		fprintf( fasta_file_pointer, ">%s\n", sequence_names[sample_counter]);
 		for(snp_counter=0; snp_counter< number_of_snps; snp_counter++)
 		{
-			fprintf( fasta_file_pointer, "%c", bases_for_snps[snp_counter][sample_counter]);
+			fputc( bases_for_snps[snp_counter][sample_counter], fasta_file_pointer );
 		}
 		fprintf( fasta_file_pointer, "\n");
 	}
   fclose(fasta_file_pointer);
-	free(base_filename);
 }

src/main.c

@@ -73,7 +73,7 @@ int main (int argc, char **argv) {
           output_phylip_file = 1;
           break;
 	      case 'o':
-          memcpy(output_filename, optarg, size_of_string(optarg) +1);
+          strncpy(output_filename, optarg, FILENAME_MAX);
 	        break;
         case 'h':
           print_usage();
@@ -84,8 +84,8 @@ int main (int argc, char **argv) {
 
   if(optind < argc)
   {
-    memcpy(multi_fasta_filename, argv[optind], size_of_string(argv[optind]) +1);
-		generate_snp_sites(multi_fasta_filename, output_multi_fasta_file, output_vcf_file, output_phylip_file, output_filename);
+    strncpy(multi_fasta_filename, argv[optind], FILENAME_MAX); 
+    generate_snp_sites(multi_fasta_filename, output_multi_fasta_file, output_vcf_file, output_phylip_file, output_filename);
   }
   else
   {

src/phylib-of-snp-sites.c

@@ -27,29 +27,25 @@
 
 void create_phylib_of_snp_sites(char filename[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples)
 {
-	FILE *fasta_file_pointer;
+	FILE *phylip_file_pointer;
 	int sample_counter;
 	int snp_counter;
-	char * base_filename;
-
-	base_filename = (char *) calloc(FILENAME_MAX,sizeof(char));
-	memcpy(base_filename, filename, FILENAME_MAX*sizeof(char));
-	fasta_file_pointer = fopen(base_filename, "w");
+
+	phylip_file_pointer = fopen(filename, "w");
 
-	fprintf( fasta_file_pointer, "%d %d\n", number_of_samples, number_of_snps);
+	fprintf( phylip_file_pointer, "%d %d\n", number_of_samples, number_of_snps);
 
 	for(sample_counter=0; sample_counter< number_of_samples; sample_counter++)
 	{
 		// sequence_name can be more than 10 (relaxed phylib format) and contain [\w\s]
 		//TODO check for illegal characters [^\w\s]
-		fprintf( fasta_file_pointer, "%s\t", sequence_names[sample_counter]);
+		fprintf( phylip_file_pointer, "%s\t", sequence_names[sample_counter]);
 
 		for(snp_counter=0; snp_counter< number_of_snps; snp_counter++)
 		{
-			fprintf( fasta_file_pointer, "%c", bases_for_snps[snp_counter][sample_counter]);
+			fputc( bases_for_snps[snp_counter][sample_counter], phylip_file_pointer);
 		}
-		fprintf( fasta_file_pointer, "\n");
+		fprintf( phylip_file_pointer, "\n");
 	}
-  fclose(fasta_file_pointer);
-	free(base_filename);
+  fclose(phylip_file_pointer);
 }

src/snp-sites.c

@@ -29,7 +29,7 @@
 #include "phylib-of-snp-sites.h"
 #include "parse-phylip.h"
 #include "string-cat.h"
-
+#include "fasta-of-snp-sites.h"
 
 void build_snp_locations(int snp_locations[], char reference_sequence[])
 {
@@ -90,54 +90,45 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
 	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 );
+	strncpy(output_filename_base, filename_without_directory, FILENAME_MAX);
 
 	if(output_filename != NULL && *output_filename != '\0')
 	{
-		memcpy(output_filename_base,output_filename, size_of_string(output_filename)+1 );
+		strncpy(output_filename_base, output_filename, FILENAME_MAX);
 	}
 
 	if(output_vcf_file)
 	{
-		char * vcf_output_filename;
-		vcf_output_filename = calloc(FILENAME_MAX,sizeof(char));
-		memcpy(vcf_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
+		char vcf_output_filename[FILENAME_MAX];
+		strncpy(vcf_output_filename, output_filename_base, FILENAME_MAX);
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
-			char extension[5] = {".vcf"};
-			concat_strings_created_with_malloc(vcf_output_filename,extension);
+			strcat(vcf_output_filename, ".vcf");
 		}
 
 	  create_vcf_file(vcf_output_filename, snp_locations, number_of_snps, bases_for_snps, sequence_names, number_of_samples, length_of_genome);
-		free(vcf_output_filename);
   }
 
   if(output_phylip_file)
   {
-		char *phylip_output_filename;
-		phylip_output_filename = calloc(FILENAME_MAX,sizeof(char));
-		memcpy(phylip_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
+		char phylip_output_filename[FILENAME_MAX];
+		strncpy(phylip_output_filename, output_filename_base, FILENAME_MAX);
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
-			char extension[10] = {".phylip"};
-			concat_strings_created_with_malloc(phylip_output_filename,extension);
+			strcat(phylip_output_filename, ".phylip");
 		}
 	  create_phylib_of_snp_sites(phylip_output_filename, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
-		free(phylip_output_filename);
   }
 
   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(FILENAME_MAX,sizeof(char));
-		memcpy(multi_fasta_output_filename, output_filename_base, (FILENAME_MAX)*sizeof(char));
+		char multi_fasta_output_filename[FILENAME_MAX];
+		strncpy(multi_fasta_output_filename, output_filename_base, FILENAME_MAX);
 		if((output_vcf_file + output_phylip_file + output_multi_fasta_file) > 1 || (output_filename == NULL || *output_filename == '\0') )
 		{
-			char extension[20] = {".snp_sites.aln"};
-			concat_strings_created_with_malloc(multi_fasta_output_filename,extension);
+			strcat(multi_fasta_output_filename, ".snp_sites.aln");
 		}
 	  create_fasta_of_snp_sites(multi_fasta_output_filename, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
-	  free(multi_fasta_output_filename);
   }
 
   // free memory

src/string-cat.c

@@ -22,21 +22,3 @@
 #include <stdlib.h>
 #include <string.h>
 
-
-int size_of_string(char *input_string)
-{
-	int i = 0;
-
-	while( input_string[i] != '\0')
-	{
-		i++;
-	}
-	return i;
-}
-
-void concat_strings_created_with_malloc(char *input_string, char *string_to_concat)
-{
-	int input_str_size = size_of_string(input_string);
-	int to_concat_str_size = size_of_string(string_to_concat);
-	memcpy(input_string + input_str_size, string_to_concat, (to_concat_str_size+1)*sizeof(char));
-}

src/string-cat.h

@@ -22,7 +22,6 @@
 #define _STRING_CAT_H_
 
 void concat_strings_created_with_malloc(char *input_string, char *string_to_concat);
-int size_of_string(char *input_string);
 
 #endif