Merge pull request #20 from sanger-pathogens/BT_add_vcf_sequence_length

Add reference sequence length to VCF output

Author: aslett1

VERSION

@@ -1 +1 @@
-2.0.0
+2.0.1

src/snp-sites.c

@@ -108,7 +108,7 @@ int generate_snp_sites(char filename[],int output_multi_fasta_file, int output_v
 			concat_strings_created_with_malloc(vcf_output_filename,extension);
 		}
 
-	  create_vcf_file(vcf_output_filename, snp_locations, number_of_snps, bases_for_snps, sequence_names, number_of_samples);
+	  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);
   }
 

src/vcf.c

@@ -28,15 +28,15 @@
 #include "snp-sites.h"
 #include <assert.h>
 
-void create_vcf_file(char filename[], int snp_locations[],int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples)
+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)
 {
 	FILE *vcf_file_pointer;
 	char * base_filename;
 	base_filename = (char *) malloc(MAX_FILENAME_SIZE*sizeof(char));
 	strcpy(base_filename, filename);
 
 	vcf_file_pointer=fopen(base_filename, "w");
-	output_vcf_header(vcf_file_pointer,sequence_names, number_of_samples);
+	output_vcf_header(vcf_file_pointer,sequence_names, number_of_samples, length_of_genome);
 	output_vcf_snps(vcf_file_pointer, bases_for_snps, snp_locations, number_of_snps, number_of_samples);
   fclose(vcf_file_pointer);
 	free(base_filename);
@@ -51,10 +51,11 @@ void output_vcf_snps(FILE * vcf_file_pointer, char ** bases_for_snps, int * snp_
 	}
 }
 
-void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int number_of_samples)
+void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int number_of_samples, size_t length_of_genome)
 {
 	int i;
 	fprintf( vcf_file_pointer, "##fileformat=VCFv4.1\n" );	
+	fprintf( vcf_file_pointer, "##contig=<ID=1,length=%i>\n", length_of_genome );	
 	fprintf( vcf_file_pointer, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n" );	
 	fprintf( vcf_file_pointer, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" );
 

src/vcf.h

@@ -21,8 +21,8 @@
 #ifndef _VCF_H_
 #define _VCF_H_
 
-void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int number_of_samples);
-void create_vcf_file(char filename[], int snp_locations[], int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples);
+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);
 void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_location, int number_of_samples);
 void output_vcf_row_samples_bases(FILE * vcf_file_pointer, char reference_base, char * alt_bases, char * bases_for_snp, int number_of_samples);

tests/data/alignment_file_one_line_per_sequence.aln.vcf

@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##contig=<ID=1,length=2000>
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	2956_6_1	2956_6_2	2956_6_3	2956_6_4	2956_6_5	2956_6_6	3002_8_1	3002_8_2	3002_8_3	3002_8_4	3002_8_5	3002_8_6	3002_8_7	4056_2_10	4056_2_11	4056_2_1	4056_2_12	4056_2_2	4056_2_3	4056_2_4	4056_2_5	4056_2_6	4056_2_7	4056_2_9	4056_6_10	4056_6_11	4056_6_12	4056_6_2	4056_6_3	4056_6_4	4056_6_5	4056_6_6	4056_6_7	4056_6_9	4056_7_10	4056_7_11	4056_7_1	4056_7_12	4056_7_7	4056_7_8	4056_7_9	4056_8_10	4056_8_1	4056_8_12	4056_8_2	4056_8_3	4056_8_4	4056_8_6	4056_8_8	4056_8_9	4075_3_11	4075_3_12	4075_3_2	4075_3_3	4075_3_5	4075_3_6	4075_3_7	4075_3_8	4075_3_9	4370_2_11	4370_2_12	4370_2_2	4370_2_3	4370_2_4	4370_2_7	4370_2_8	4370_2_9	4370_3_11	4370_3_1	4370_3_6	4370_3_7	4370_3_8	5174_5_1	5174_5_2	5174_5_3	5174_5_4	5174_5_5	5174_5_6	5174_5_7	5174_5_9	5174_6_10	5174_6_1	5174_6_2	5174_6_3	5174_6_4	5174_6_5	5174_6_6	5174_6_7	5174_6_8	5174_6_9	5174_7_10	5174_7_1	5174_7_2	5174_7_3	5174_7_4	5174_7_5	5174_7_6	5174_7_7	5174_7_8	5174_7_9	5174_8_1	5174_8_2	5174_8_3	5174_8_5	5174_8_6	5174_8_8	5174_8_9	Vibrio_parahaemolyticus	Vibrio_vulnificus	
 1	825	.	A	G	.	.	.	GT	0	0	0	0	0	0	1	1	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0

tests/data/alignment_file_with_n.aln.vcf

@@ -1,4 +1,5 @@
 ##fileformat=VCFv4.1
+##contig=<ID=1,length=2000>
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	2956_6_1	2956_6_2	2956_6_3	2956_6_4	2956_6_5	2956_6_6	3002_8_1	3002_8_2	3002_8_3	3002_8_4	3002_8_5	3002_8_6	3002_8_7	4056_2_10	4056_2_11	4056_2_1	4056_2_12	4056_2_2	4056_2_3	4056_2_4	4056_2_5	4056_2_6	4056_2_7	4056_2_9	4056_6_10	4056_6_11	4056_6_12	4056_6_2	4056_6_3	4056_6_4	4056_6_5	4056_6_6	4056_6_7	4056_6_9	4056_7_10	4056_7_11	4056_7_1	4056_7_12	4056_7_7	4056_7_8	4056_7_9	4056_8_10	4056_8_1	4056_8_12	4056_8_2	4056_8_3	4056_8_4	4056_8_6	4056_8_8	4056_8_9	4075_3_11	4075_3_12	4075_3_2	4075_3_3	4075_3_5	4075_3_6	4075_3_7	4075_3_8	4075_3_9	4370_2_11	4370_2_12	4370_2_2	4370_2_3	4370_2_4	4370_2_7	4370_2_8	4370_2_9	4370_3_11	4370_3_1	4370_3_6	4370_3_7	4370_3_8	5174_5_1	5174_5_2	5174_5_3	5174_5_4	5174_5_5	5174_5_6	5174_5_7	5174_5_9	5174_6_10	5174_6_1	5174_6_2	5174_6_3	5174_6_4	5174_6_5	5174_6_6	5174_6_7	5174_6_8	5174_6_9	5174_7_10	5174_7_1	5174_7_2	5174_7_3	5174_7_4	5174_7_5	5174_7_6	5174_7_7	5174_7_8	5174_7_9	5174_8_1	5174_8_2	5174_8_3	5174_8_5	5174_8_6	5174_8_8	5174_8_9	Vibrio_parahaemolyticus	Vibrio_vulnificus	
 1	825	.	A	G	.	.	.	GT	0	0	0	0	0	0	1	1	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0