From ab47c064596103670e9ccefd43071a5fe0d94156 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Tue, 14 Jul 2015 16:35:28 +0100
Subject: [PATCH 1/8] Add bounds check on the number of alternative bases

There was an assumption that there would not be greater than 15
different characters used in a given position between sequences.  This
is unlikely to be possible in well formatted files but it could be the
case in an input file is corrupted.
---
 src/vcf.c | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/src/vcf.c b/src/vcf.c
index e918828..f96ba39 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -27,7 +27,7 @@
 #include "alignment-file.h"
 #include "snp-sites.h"
 
-
+const int MAXIMUM_NUMBER_OF_ALT_BASES = 30;
 
 void create_vcf_file(char filename[], int snp_locations[],int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples)
 {
@@ -69,7 +69,7 @@ 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];
+	char alt_bases[MAXIMUM_NUMBER_OF_ALT_BASES];
 	if(reference_base == '\0')
 	{
 		return;	
@@ -122,6 +122,12 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 		{
 			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 - 2)
+				{
+					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] = ',';

From 48349309409a6281b2013cbfcb7130fe2e58a790 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Tue, 14 Jul 2015 16:37:49 +0000
Subject: [PATCH 2/8] add format_alternative_bases

---
 src/Makefile.am       |  1 +
 src/vcf.c             | 29 +++++++++++++++++++--
 src/vcf.h             |  2 ++
 tests/check-vcf.c     | 60 +++++++++++++++++++++++++++++++++++++++++++
 tests/check-vcf.h     | 28 ++++++++++++++++++++
 tests/run-all-tests.c | 15 +++++++++--
 6 files changed, 131 insertions(+), 4 deletions(-)
 create mode 100644 tests/check-vcf.c
 create mode 100644 tests/check-vcf.h

diff --git a/src/Makefile.am b/src/Makefile.am
index cf94178..8436241 100644
--- 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
index f96ba39..64b9d80 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -27,8 +27,6 @@
 #include "alignment-file.h"
 #include "snp-sites.h"
 
-const int MAXIMUM_NUMBER_OF_ALT_BASES = 30;
-
 void create_vcf_file(char filename[], int snp_locations[],int number_of_snps, char ** bases_for_snps, char ** sequence_names, int number_of_samples)
 {
 	FILE *vcf_file_pointer;
@@ -145,6 +143,33 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 	}
 }
 
+char * format_alternative_bases(char * alt_bases)
+{
+	char * formatted_alt_bases = malloc(MAXIMUM_NUMBER_OF_ALT_BASES*2*sizeof(char));
+	int i;
+	for (i = 0; i < MAXIMUM_NUMBER_OF_ALT_BASES; i++)
+	{
+		if (alt_bases[i] == '\0')
+		{
+			if (i == 0)
+			{
+				formatted_alt_bases[0] = '\0';
+			}
+			else
+			{
+				formatted_alt_bases[i*2 - 1] = '\0';
+			}
+			break;
+		}
+		else
+		{
+			formatted_alt_bases[i*2] = alt_bases[i];
+			formatted_alt_bases[i*2 + 1] = ',';
+		}
+	}
+	return formatted_alt_bases;
+}
+
 int check_if_char_in_string(char search_string[], char target_char, int search_string_length)
 {
 	int i;
diff --git a/src/vcf.h b/src/vcf.h
index 764f5d1..9cddba3 100644
--- a/src/vcf.h
+++ b/src/vcf.h
@@ -27,7 +27,9 @@ void output_vcf_snps(FILE * vcf_file_pointer, char ** bases_for_snps, int * snp_
 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);
+char * format_alternative_bases(char * alt_bases);
 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
new file mode 100644
index 0000000..731f2b9
--- /dev/null
+++ b/tests/check-vcf.c
@@ -0,0 +1,60 @@
+/*
+ *  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_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
+
+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, format_alternative_bases_test);
+  suite_add_tcase (s, tc_vcf_file);
+
+  return s;
+}
+
+
+
diff --git a/tests/check-vcf.h b/tests/check-vcf.h
new file mode 100644
index 0000000..6b11178
--- /dev/null
+++ b/tests/check-vcf.h
@@ -0,0 +1,28 @@
+/*
+ *  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_format_alternative_bases(char *, char *);
+Suite * vcf_suite (void);
+#endif
+
+
+
diff --git a/tests/run-all-tests.c b/tests/run-all-tests.c
index 2ee66d1..f9faee6 100644
--- 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;
 }

From dca6f466bf9cf10e213583e79d76b3205f150f95 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Wed, 15 Jul 2015 12:09:49 +0000
Subject: [PATCH 3/8] Track simple list of alleles, reformat in output

---
 src/vcf.c | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/src/vcf.c b/src/vcf.c
index 64b9d80..0257fa4 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -89,7 +89,9 @@ void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_locat
 	// 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 * 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");
@@ -128,19 +130,10 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 				}
 				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] == ',')
-	{
-		alt_bases[num_alt_bases-1] = '\0';
-	}
-	else
-	{
-		alt_bases[num_alt_bases] = '\0';
-	}
+	alt_bases[num_alt_bases] = '\0';
 }
 
 char * format_alternative_bases(char * alt_bases)

From 3b27b408dd95de39c982423899b760023ed70f92 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Wed, 15 Jul 2015 15:46:16 +0000
Subject: [PATCH 4/8] Add method to calculate GT formatted allele

GT format reports the index into a list of alleles rather than the
relevant allele
---
 src/vcf.c         | 29 +++++++++++++++++++++++++++++
 src/vcf.h         |  3 ++-
 tests/check-vcf.c | 31 +++++++++++++++++++++++++++++++
 tests/check-vcf.h |  1 +
 4 files changed, 63 insertions(+), 1 deletion(-)

diff --git a/src/vcf.c b/src/vcf.c
index 0257fa4..d49e253 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -136,6 +136,35 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 	alt_bases[num_alt_bases] = '\0';
 }
 
+char * format_allele_index(char base, char reference_base, char * alt_bases)
+{
+	int maximum_format_length = (int) log10((double) MAXIMUM_NUMBER_OF_ALT_BASES) + 1;
+	char * result = malloc((maximum_format_length + 1)*sizeof(char));
+	int index;
+	if (reference_base == base)
+	{
+		sprintf(result, "0");
+	}
+	else
+	{
+		sprintf(result, ".");
+		for (index = 1; index<MAXIMUM_NUMBER_OF_ALT_BASES; index++)
+		{
+			if (alt_bases[index-1] == base)
+			{
+				sprintf(result, "%i", index);
+				break;
+			}
+			if (alt_bases[index-1] == '\0')
+			{
+				sprintf(result, ".");
+				break;
+			}
+		}
+	}
+	return result;
+}
+
 char * format_alternative_bases(char * alt_bases)
 {
 	char * formatted_alt_bases = malloc(MAXIMUM_NUMBER_OF_ALT_BASES*2*sizeof(char));
diff --git a/src/vcf.h b/src/vcf.h
index 9cddba3..239c72d 100644
--- a/src/vcf.h
+++ b/src/vcf.h
@@ -27,7 +27,8 @@ void output_vcf_snps(FILE * vcf_file_pointer, char ** bases_for_snps, int * snp_
 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);
-char * format_alternative_bases(char * alt_bases);
+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
diff --git a/tests/check-vcf.c b/tests/check-vcf.c
index 731f2b9..62af693 100644
--- a/tests/check-vcf.c
+++ b/tests/check-vcf.c
@@ -45,12 +45,43 @@ START_TEST (format_alternative_bases_test)
 }
 END_TEST
 
+void check_format_allele_index(char test_base, char reference_base, char alt_bases_array[], char expected_result_array[])
+{
+  char * result;
+  char * alt_bases = malloc(50*sizeof(char));
+  strcpy(alt_bases, alt_bases_array);
+  char * expected_result = malloc(20*sizeof(char));
+  strcpy(expected_result, expected_result_array);
+  result = format_allele_index(test_base, reference_base, alt_bases);
+  ck_assert_str_eq(result, expected_result);
+  free(result);
+  free(alt_bases);
+  free(expected_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");
+}
+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, 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
index 6b11178..0dc7ef4 100644
--- a/tests/check-vcf.h
+++ b/tests/check-vcf.h
@@ -21,6 +21,7 @@
 #define _CHECK_VCF_H_
 
 void check_format_alternative_bases(char *, char *);
+void check_format_allele_index(char, char, char[], char[]);
 Suite * vcf_suite (void);
 #endif
 

From 09dee85f9b675fcabccfb64b80ea395864add778 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Thu, 16 Jul 2015 10:45:38 +0000
Subject: [PATCH 5/8] Update output format to show Genotype

The previous behaviour output an Alt Base which was not understood by
some other tools.  This changes the format to GT.
---
 src/vcf.c                                     | 27 ++++++++-----------
 src/vcf.h                                     |  2 +-
 tests/check-vcf.c                             |  4 +++
 ...ignment_file_one_line_per_sequence.aln.vcf | 12 ++++-----
 tests/data/alignment_file_with_n.aln.vcf      | 12 ++++-----
 5 files changed, 28 insertions(+), 29 deletions(-)

diff --git a/src/vcf.c b/src/vcf.c
index d49e253..d26af30 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -54,7 +54,7 @@ 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++)
@@ -99,14 +99,14 @@ void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_locat
 	// 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 );
 	
 	fprintf( vcf_file_pointer, "\n");	
 }
@@ -141,7 +141,7 @@ char * format_allele_index(char base, char reference_base, char * alt_bases)
 	int maximum_format_length = (int) log10((double) MAXIMUM_NUMBER_OF_ALT_BASES) + 1;
 	char * result = malloc((maximum_format_length + 1)*sizeof(char));
 	int index;
-	if (reference_base == base)
+	if (reference_base == base || toupper(base) == 'N' || base == '-')
 	{
 		sprintf(result, "0");
 	}
@@ -157,7 +157,6 @@ char * format_allele_index(char base, char reference_base, char * alt_bases)
 			}
 			if (alt_bases[index-1] == '\0')
 			{
-				sprintf(result, ".");
 				break;
 			}
 		}
@@ -205,20 +204,16 @@ 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
index 239c72d..b60bce9 100644
--- a/src/vcf.h
+++ b/src/vcf.h
@@ -25,7 +25,7 @@ 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 output_vcf_row_samples_bases(FILE * vcf_file_pointer, char reference_base, char * alt_bases, 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);
 char * format_alternative_bases(char *);
 char * format_allele_index(char, char, char *);
diff --git a/tests/check-vcf.c b/tests/check-vcf.c
index 62af693..c836fd8 100644
--- a/tests/check-vcf.c
+++ b/tests/check-vcf.c
@@ -72,6 +72,10 @@ START_TEST (format_allele_index_test)
   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
 
diff --git a/tests/data/alignment_file_one_line_per_sequence.aln.vcf b/tests/data/alignment_file_one_line_per_sequence.aln.vcf
index 590e89a..d4a88eb 100644
--- 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
index 590e89a..d4a88eb 100644
--- 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

From f4f5e0871b724e25e2bf19f858f2940beb7ec336 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Thu, 16 Jul 2015 12:52:29 +0100
Subject: [PATCH 6/8] Bump VERSION

---
 VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/VERSION b/VERSION
index d00491f..227cea2 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1
+2.0.0

From d78487d52a8cc351f051d7abbb7ec648f4a74a07 Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Thu, 16 Jul 2015 12:27:36 +0000
Subject: [PATCH 7/8] Tidy up check_format_allele_index

---
 tests/check-vcf.c | 8 +-------
 tests/check-vcf.h | 2 +-
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/tests/check-vcf.c b/tests/check-vcf.c
index c836fd8..102284f 100644
--- a/tests/check-vcf.c
+++ b/tests/check-vcf.c
@@ -45,18 +45,12 @@ START_TEST (format_alternative_bases_test)
 }
 END_TEST
 
-void check_format_allele_index(char test_base, char reference_base, char alt_bases_array[], char expected_result_array[])
+void check_format_allele_index(char test_base, char reference_base, char * alt_bases, char * expected_result)
 {
   char * result;
-  char * alt_bases = malloc(50*sizeof(char));
-  strcpy(alt_bases, alt_bases_array);
-  char * expected_result = malloc(20*sizeof(char));
-  strcpy(expected_result, expected_result_array);
   result = format_allele_index(test_base, reference_base, alt_bases);
   ck_assert_str_eq(result, expected_result);
   free(result);
-  free(alt_bases);
-  free(expected_result);
 }
 
 START_TEST (format_allele_index_test)
diff --git a/tests/check-vcf.h b/tests/check-vcf.h
index 0dc7ef4..3274bfb 100644
--- a/tests/check-vcf.h
+++ b/tests/check-vcf.h
@@ -21,7 +21,7 @@
 #define _CHECK_VCF_H_
 
 void check_format_alternative_bases(char *, char *);
-void check_format_allele_index(char, char, char[], char[]);
+void check_format_allele_index(char, char, char *, char *);
 Suite * vcf_suite (void);
 #endif
 

From 497b6e0b56710a552b23bd2ac34015a18e5a574f Mon Sep 17 00:00:00 2001
From: Ben Taylor <ben.taylor@sanger.ac.uk>
Date: Thu, 16 Jul 2015 14:39:01 +0000
Subject: [PATCH 8/8] Simplify vcf code with calloc

Use calloc and strlen to simplify the vcf related code
---
 src/vcf.c         | 49 +++++++++++++++++------------------------------
 src/vcf.h         |  2 +-
 tests/check-vcf.c | 15 +++++++++++++++
 tests/check-vcf.h |  1 +
 4 files changed, 35 insertions(+), 32 deletions(-)

diff --git a/src/vcf.c b/src/vcf.c
index d26af30..46a7cea 100644
--- a/src/vcf.c
+++ b/src/vcf.c
@@ -26,6 +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)
 {
@@ -67,7 +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[MAXIMUM_NUMBER_OF_ALT_BASES];
 	if(reference_base == '\0')
 	{
 		return;	
@@ -88,7 +88,7 @@ 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);
+	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);
@@ -107,22 +107,24 @@ void output_vcf_row(FILE * vcf_file_pointer, char * bases_for_snp, int snp_locat
 	
 	// Bases for each sample
 	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 - 2)
+				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);
@@ -133,13 +135,14 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 			}
 		}
 	}
-	alt_bases[num_alt_bases] = '\0';
+	return alt_bases;
 }
 
 char * format_allele_index(char base, char reference_base, char * alt_bases)
 {
-	int maximum_format_length = (int) log10((double) MAXIMUM_NUMBER_OF_ALT_BASES) + 1;
-	char * result = malloc((maximum_format_length + 1)*sizeof(char));
+	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 == '-')
 	{
@@ -148,17 +151,13 @@ char * format_allele_index(char base, char reference_base, char * alt_bases)
 	else
 	{
 		sprintf(result, ".");
-		for (index = 1; index<MAXIMUM_NUMBER_OF_ALT_BASES; index++)
+		for (index = 1; index <= length_of_alt_bases; index++)
 		{
 			if (alt_bases[index-1] == base)
 			{
 				sprintf(result, "%i", index);
 				break;
 			}
-			if (alt_bases[index-1] == '\0')
-			{
-				break;
-			}
 		}
 	}
 	return result;
@@ -166,27 +165,15 @@ char * format_allele_index(char base, char reference_base, char * alt_bases)
 
 char * format_alternative_bases(char * alt_bases)
 {
-	char * formatted_alt_bases = malloc(MAXIMUM_NUMBER_OF_ALT_BASES*2*sizeof(char));
+	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;
-	for (i = 0; i < MAXIMUM_NUMBER_OF_ALT_BASES; i++)
+	formatted_alt_bases[0] = alt_bases[0];
+	for (i = 1; i < number_of_alt_bases; i++)
 	{
-		if (alt_bases[i] == '\0')
-		{
-			if (i == 0)
-			{
-				formatted_alt_bases[0] = '\0';
-			}
-			else
-			{
-				formatted_alt_bases[i*2 - 1] = '\0';
-			}
-			break;
-		}
-		else
-		{
-			formatted_alt_bases[i*2] = alt_bases[i];
-			formatted_alt_bases[i*2 + 1] = ',';
-		}
+		formatted_alt_bases[i*2 - 1] = ',';
+		formatted_alt_bases[i*2] = alt_bases[i];
 	}
 	return formatted_alt_bases;
 }
diff --git a/src/vcf.h b/src/vcf.h
index b60bce9..51affe4 100644
--- a/src/vcf.h
+++ b/src/vcf.h
@@ -26,7 +26,7 @@ void create_vcf_file(char filename[], int snp_locations[], int number_of_snps, c
 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);
-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);
 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);
diff --git a/tests/check-vcf.c b/tests/check-vcf.c
index 102284f..8ae95cf 100644
--- a/tests/check-vcf.c
+++ b/tests/check-vcf.c
@@ -28,6 +28,20 @@
 #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;
@@ -78,6 +92,7 @@ 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);
diff --git a/tests/check-vcf.h b/tests/check-vcf.h
index 3274bfb..99f3167 100644
--- a/tests/check-vcf.h
+++ b/tests/check-vcf.h
@@ -20,6 +20,7 @@
 #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);