Merge pull request #19 from sanger-pathogens/BT5_471874_GT_format

Change output format to show Genotype rather than Alt Base
sanger-pathogens · Jul 16, 2015 · 3451d0a · 3451d0a
2 parents 682941d + 497b6e0
commit 3451d0a
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Showing 9 changed files with 226 additions and 42 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1
+2.0.0
diff --git a/src/Makefile.am b/src/Makefile.am
@@ -25,6 +25,7 @@ TESTS = $(check_PROGRAMS)
 check_PROGRAMS = run-all-tests
 run_all_tests_SOURCES = \
 	../tests/check-snp-sites.c \
+	../tests/check-vcf.c \
 	../tests/helper-methods.c \
 	../tests/run-all-tests.c
 run_all_tests_CFLAGS = -I../tests

diff --git a/src/vcf.c b/src/vcf.c
@@ -26,8 +26,7 @@
 #include "vcf.h"
 #include "alignment-file.h"
 #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)
 {
@@ -56,7 +55,7 @@ void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int num
 {
 	int i;
 	fprintf( vcf_file_pointer, "##fileformat=VCFv4.1\n" );	
-	fprintf( vcf_file_pointer, "##INFO=<ID=AB,Number=1,Type=String,Description=\"Alt Base\">\n" );
+	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" );
 
 	for(i=0; i<number_of_samples; i++)
@@ -69,7 +68,6 @@ void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int num
 void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_location, int number_of_samples)
 {
 	char reference_base =  bases_for_snp[0];
-	char alt_bases[30];
 	if(reference_base == '\0')
 	{
 		return;	
@@ -90,53 +88,94 @@ void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_locat
 	// ALT
 	// Need to look through list and find unique characters
 
-	alternative_bases(reference_base, bases_for_snp, alt_bases, number_of_samples);
-	fprintf( vcf_file_pointer, "%s\t", alt_bases);
+	char * alt_bases = alternative_bases(reference_base, bases_for_snp, number_of_samples);
+	char * alternative_bases_string = format_alternative_bases(alt_bases);
+	fprintf( vcf_file_pointer, "%s\t", alternative_bases_string );
+	free(alternative_bases_string);
 
 	// QUAL
 	fprintf( vcf_file_pointer, ".\t");
 
 	// FILTER
 	fprintf( vcf_file_pointer, ".\t");
 
-	// FORMAT
-	fprintf( vcf_file_pointer, "AB\t");
-
 	// INFO
 	fprintf( vcf_file_pointer, ".\t");
 
+	// FORMAT
+	fprintf( vcf_file_pointer, "GT\t");
+
 	// Bases for each sample
-	output_vcf_row_samples_bases(vcf_file_pointer, reference_base, bases_for_snp, number_of_samples );
+	output_vcf_row_samples_bases(vcf_file_pointer, reference_base, alt_bases, bases_for_snp, number_of_samples );
+	free(alt_bases);
 
 	fprintf( vcf_file_pointer, "\n");	
 }
 
 
-void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases[], int number_of_samples)
+char * alternative_bases(char reference_base, char * bases_for_snp, int number_of_samples)
 {
 	int i;
 	int num_alt_bases = 0;
+	char * alt_bases = calloc(MAXIMUM_NUMBER_OF_ALT_BASES+1, sizeof(char));
 	for(i=0; i< number_of_samples; i++ )
 	{
 		if((bases_for_snp[i] != reference_base) && (bases_for_snp[i] != '-') && (toupper(bases_for_snp[i]) != 'N') )
 		{
 			if(check_if_char_in_string(alt_bases, bases_for_snp[i], num_alt_bases) == 0)
 			{
+				if (num_alt_bases >= MAXIMUM_NUMBER_OF_ALT_BASES)
+				{
+					fprintf(stderr, "Unexpectedly large number of alternative bases found between sequences.  Please check input file is not corrupted\n\n");
+					fflush(stderr);
+					exit(EXIT_FAILURE);
+				}
 				alt_bases[num_alt_bases] = bases_for_snp[i];
 				num_alt_bases++;
-				alt_bases[num_alt_bases] = ',';
-				num_alt_bases++;
 			}
 		}
 	}
-	if(num_alt_bases > 0 && alt_bases[num_alt_bases-1] == ',')
+	return alt_bases;
+}
+
+char * format_allele_index(char base, char reference_base, char * alt_bases)
+{
+	int length_of_alt_bases = strlen(alt_bases);
+	assert(length_of_alt_bases < 100);
+	char * result = calloc(3, sizeof(char));
+	int index;
+	if (reference_base == base || toupper(base) == 'N' || base == '-')
 	{
-		alt_bases[num_alt_bases-1] = '\0';
+		sprintf(result, "0");
 	}
 	else
 	{
-		alt_bases[num_alt_bases] = '\0';
+		sprintf(result, ".");
+		for (index = 1; index <= length_of_alt_bases; index++)
+		{
+			if (alt_bases[index-1] == base)
+			{
+				sprintf(result, "%i", index);
+				break;
+			}
+		}
+	}
+	return result;
+}
+
+char * format_alternative_bases(char * alt_bases)
+{
+	int number_of_alt_bases = strlen(alt_bases);
+	assert( number_of_alt_bases < MAXIMUM_NUMBER_OF_ALT_BASES );
+	char * formatted_alt_bases = calloc(number_of_alt_bases*2 + 1, sizeof(char));
+	int i;
+	formatted_alt_bases[0] = alt_bases[0];
+	for (i = 1; i < number_of_alt_bases; i++)
+	{
+		formatted_alt_bases[i*2 - 1] = ',';
+		formatted_alt_bases[i*2] = alt_bases[i];
 	}
+	return formatted_alt_bases;
 }
 
 int check_if_char_in_string(char search_string[], char target_char, int search_string_length)
@@ -152,20 +191,16 @@ int check_if_char_in_string(char search_string[], char target_char, int search_s
 	return 0;
 }
 
-void output_vcf_row_samples_bases(FILE * vcf_file_pointer, char reference_base, char * bases_for_snp, 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)
 {
 	int i;
+	char * format;
 
 	for(i=0; i < number_of_samples ; i++ )
 	{
-		if((bases_for_snp[i] == reference_base) || (bases_for_snp[i] == '-') || (toupper(bases_for_snp[i]) == 'N') )
-		{
-			fprintf( vcf_file_pointer, "." );	
-		}
-		else
-		{
-			fprintf( vcf_file_pointer, "%c", (char) bases_for_snp[i] );	
-		}
+		format = format_allele_index(bases_for_snp[i], reference_base, alt_bases);
+		fprintf( vcf_file_pointer, "%s", format);	
+		free(format);
 		if(i+1 != number_of_samples)
 		{
 			fprintf( vcf_file_pointer, "\t");

diff --git a/src/vcf.h b/src/vcf.h
@@ -25,9 +25,12 @@ void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int num
 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_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 * bases_for_snp, int number_of_samples);
-void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases[], 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);
+char * alternative_bases(char reference_base, char * bases_for_snp, int number_of_samples);
+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
diff --git a/tests/check-vcf.c b/tests/check-vcf.c
@@ -0,0 +1,104 @@
+/*
+ *  Wellcome Trust Sanger Institute
+ *  Copyright (C) 2013  Wellcome Trust Sanger Institute
+ *  
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 3
+ *  of the License, or (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *  
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, write to the Free Software
+ *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <check.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include "check-vcf.h"
+#include "vcf.h"
+
+void check_alternative_bases(char reference_base, char * bases_for_snp, int number_of_samples, char * expected_result)
+{
+  char * result;
+  result = alternative_bases(reference_base, bases_for_snp, number_of_samples);
+  ck_assert_str_eq(result, expected_result);
+  free(result);
+}
+
+START_TEST (alternative_bases_test)
+{
+  check_alternative_bases('A', "AGCT-nN", 6, "GCT");
+}
+END_TEST
+
+void check_format_alternative_bases(char * test_case, char * expected_result)
+{
+  char * result;
+  result = format_alternative_bases(test_case);
+  ck_assert_str_eq(result, expected_result);
+  free(result);
+}
+
+START_TEST (format_alternative_bases_test)
+{
+  check_format_alternative_bases("", "");
+  check_format_alternative_bases("A", "A");
+  check_format_alternative_bases("AC", "A,C");
+  check_format_alternative_bases("ACT", "A,C,T");
+}
+END_TEST
+
+void check_format_allele_index(char test_base, char reference_base, char * alt_bases, char * expected_result)
+{
+  char * result;
+  result = format_allele_index(test_base, reference_base, alt_bases);
+  ck_assert_str_eq(result, expected_result);
+  free(result);
+}
+
+START_TEST (format_allele_index_test)
+{
+  check_format_allele_index('A', 'A', "", "0");
+  check_format_allele_index('A', 'A', "C", "0");
+  check_format_allele_index('A', 'A', "CA", "0");
+
+  check_format_allele_index('A', 'C', "A", "1");
+  check_format_allele_index('A', 'C', "GA", "2");
+
+  check_format_allele_index('A', 'C', "", ".");
+  check_format_allele_index('A', 'C', "G", ".");
+
+  check_format_allele_index('A', 'B', "CDEFGHIJKLMNOPAQRST", "15");
+
+  check_format_allele_index('-', 'A', "C", "0");
+  check_format_allele_index('N', 'A', "C", "0");
+  check_format_allele_index('n', 'A', "C", "0");
+}
+END_TEST
+
+Suite * vcf_suite (void)
+{
+  Suite *s = suite_create ("Creating_VCF_file");
+
+  TCase *tc_vcf_file = tcase_create ("vcf_file");
+  tcase_add_test (tc_vcf_file, alternative_bases_test);
+  tcase_add_test (tc_vcf_file, format_alternative_bases_test);
+  tcase_add_test (tc_vcf_file, format_allele_index_test);
+  suite_add_tcase (s, tc_vcf_file);
+
+  return s;
+}
+
+
+
diff --git a/tests/check-vcf.h b/tests/check-vcf.h
@@ -0,0 +1,30 @@
+/*
+ *  Wellcome Trust Sanger Institute
+ *  Copyright (C) 2013  Wellcome Trust Sanger Institute
+ *  
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 3
+ *  of the License, or (at your option) any later version.
+ *  
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *  
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program; if not, write to the Free Software
+ *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+
+#ifndef _CHECK_VCF_H_
+#define _CHECK_VCF_H_
+
+void check_alternative_bases(char, char *, int, char *);
+void check_format_alternative_bases(char *, char *);
+void check_format_allele_index(char, char, char *, char *);
+Suite * vcf_suite (void);
+#endif
+
+
+
diff --git a/tests/data/alignment_file_one_line_per_sequence.aln.vcf b/tests/data/alignment_file_one_line_per_sequence.aln.vcf
@@ -1,8 +1,8 @@
 ##fileformat=VCFv4.1
-##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
+##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	.	.	AB	.	.	.	.	.	.	.	G	G	.	.	.	G	.	G	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	G	G	G	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.
-1	1278	.	A	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
-1	1281	.	C	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
-1	1299	.	G	A	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A
-1	1435	.	C	T	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
+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
+1	1278	.	A	G	.	.	.	GT	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	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	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	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
+1	1281	.	C	G	.	.	.	GT	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	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	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	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
+1	1299	.	G	A	.	.	.	GT	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	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	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	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
+1	1435	.	C	T	.	.	.	GT	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	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	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	0	0	0	0	0	0	0	0	0	0	0
diff --git a/tests/data/alignment_file_with_n.aln.vcf b/tests/data/alignment_file_with_n.aln.vcf
@@ -1,8 +1,8 @@
 ##fileformat=VCFv4.1
-##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
+##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	.	.	AB	.	.	.	.	.	.	.	G	G	.	.	.	G	.	G	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	G	G	G	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.
-1	1278	.	A	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
-1	1281	.	C	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
-1	1299	.	G	A	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A
-1	1435	.	C	T	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
+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
+1	1278	.	A	G	.	.	.	GT	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	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	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	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
+1	1281	.	C	G	.	.	.	GT	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	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	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	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
+1	1299	.	G	A	.	.	.	GT	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	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	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	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
+1	1435	.	C	T	.	.	.	GT	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	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	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	0	0	0	0	0	0	0	0	0	0	0
diff --git a/tests/run-all-tests.c b/tests/run-all-tests.c
@@ -22,16 +22,27 @@
 #include <string.h>
 #include <check.h>
 #include "check-snp-sites.h"
+#include "check-vcf.h"
 
 
 
 int main (void)
 {
   int number_failed;
-  Suite *s = snp_sites_suite ();
-  SRunner *sr = srunner_create (s);
+  Suite *s;
+  SRunner *sr;
+
+  s = snp_sites_suite ();
+  sr = srunner_create (s);
   srunner_run_all (sr, CK_NORMAL);
   number_failed = srunner_ntests_failed (sr);
   srunner_free (sr);
+
+  s = vcf_suite ();
+  sr = srunner_create (s);
+  srunner_run_all (sr, CK_NORMAL);
+  number_failed += srunner_ntests_failed (sr);
+  srunner_free (sr);
+
   return (number_failed == 0) ? EXIT_SUCCESS : EXIT_FAILURE;
 }