treat N as gap

sanger-pathogens · Jan 24, 2012 · 413134d · 413134d
1 parent 0654d8a
commit 413134d
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/alignment_file.c b/alignment_file.c
@@ -175,12 +175,12 @@ int detect_snps(char reference_sequence[], char filename[], int length_of_genome
     for(i = 0; i < length_of_genome; i++)
 		{
 			// If there is an indel in the reference sequence, replace with the first proper base you find
-			if(reference_sequence[i] == '-' && seq->seq.s[i] != '-' )
+			if((reference_sequence[i] == '-' && seq->seq.s[i] != '-' ) || (toupper(reference_sequence[i]) == 'N' && seq->seq.s[i] != 'N' ))
 			{
 				reference_sequence[i] = toupper(seq->seq.s[i]);
 			}
 
-			if(reference_sequence[i] != '*' && seq->seq.s[i] != '-' && reference_sequence[i] != toupper(seq->seq.s[i]))
+			if(reference_sequence[i] != '*' && seq->seq.s[i] != '-' && toupper(seq->seq.s[i]) != 'N' && reference_sequence[i] != toupper(seq->seq.s[i]))
 			{
 				reference_sequence[i] = '*';
 				number_of_snps++;

diff --git a/parse_phylip.c b/parse_phylip.c
@@ -52,7 +52,7 @@ int does_column_contain_snps(int snp_column, char reference_base)
 			return 0;	
 		}
 
-		if(sequences[i][snp_column]  != '-' && sequences[i][snp_column] != reference_base)
+		if(sequences[i][snp_column]  != '-' && toupper(sequences[i][snp_column])  != 'N' && sequences[i][snp_column] != reference_base)
 		{
 			return 1;
 		}

diff --git a/snp_sites b/snp_sites
diff --git a/tests/check_snp_sites b/tests/check_snp_sites
diff --git a/vcf.c b/vcf.c
@@ -116,7 +116,7 @@ void alternative_bases(char reference_base, char * bases_for_snp, char alt_bases
 	int num_alt_bases = 0;
 	for(i=0; i< number_of_samples; i++ )
 	{
-		if((bases_for_snp[i] != reference_base) && (bases_for_snp[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)
 			{
@@ -156,7 +156,7 @@ void output_vcf_row_samples_bases(FILE * vcf_file_pointer, char reference_base,
 
 	for(i=0; i < number_of_samples ; i++ )
 	{
-		if((bases_for_snp[i] == reference_base) || (bases_for_snp[i] == '-'))
+		if((bases_for_snp[i] == reference_base) || (bases_for_snp[i] == '-') || (toupper(bases_for_snp[i]) == 'N') )
 		{
 			fprintf( vcf_file_pointer, "." );	
 		}