From 0654d8a28a16cd027f8fa95e7c60357f6b10e3cd Mon Sep 17 00:00:00 2001
From: andrewjpage <andrewjpage@gmail.com>
Date: Tue, 24 Jan 2012 10:23:04 +0000
Subject: [PATCH 1/2] readd test output files

---
 .gitignore                                    |   2 -
 ...ment_file_one_line_per_sequence.aln.phylip | 110 ++++++++++++++++++
 ...ignment_file_one_line_per_sequence.aln.vcf |   8 ++
 3 files changed, 118 insertions(+), 2 deletions(-)
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.phylip
 create mode 100644 tests/data/alignment_file_one_line_per_sequence.aln.vcf

diff --git a/.gitignore b/.gitignore
index aef3fc7..d63d395 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,2 @@
 *.o
 gubbins
-*.phylip
-*.vcf
diff --git a/tests/data/alignment_file_one_line_per_sequence.aln.phylip b/tests/data/alignment_file_one_line_per_sequence.aln.phylip
new file mode 100644
index 0000000..1171765
--- /dev/null
+++ b/tests/data/alignment_file_one_line_per_sequence.aln.phylip
@@ -0,0 +1,110 @@
+109 5
+2956_6_1	AACGC
+2956_6_2	AACGC
+2956_6_3	AACGC
+2956_6_4	AACGC
+2956_6_5	AACGC
+2956_6_6	AACGC
+3002_8_1	GACGC
+3002_8_2	GACGC
+3002_8_3	AACGC
+3002_8_4	AACGC
+3002_8_5	-ACGC
+3002_8_6	GACGC
+3002_8_7	AACGC
+4056_2_10	GACGC
+4056_2_11	AACGC
+4056_2_1	AACGC
+4056_2_12	AACGC
+4056_2_2	AACGC
+4056_2_3	-ACGC
+4056_2_4	GACGT
+4056_2_5	AACGC
+4056_2_6	AACGC
+4056_2_7	AACGC
+4056_2_9	AACGC
+4056_6_10	AACGC
+4056_6_11	AACGC
+4056_6_12	AACGC
+4056_6_2	AACGC
+4056_6_3	AACGC
+4056_6_4	AACGC
+4056_6_5	AACGC
+4056_6_6	AACGC
+4056_6_7	AACGC
+4056_6_9	AACGC
+4056_7_10	AACGC
+4056_7_11	AACGC
+4056_7_1	AACGC
+4056_7_12	AACGC
+4056_7_7	AACGC
+4056_7_8	AACGC
+4056_7_9	AACGC
+4056_8_10	AACGC
+4056_8_1	AACGC
+4056_8_12	AACGC
+4056_8_2	AACGC
+4056_8_3	AACGC
+4056_8_4	AACGC
+4056_8_6	GACGC
+4056_8_8	AACGC
+4056_8_9	AACGC
+4075_3_11	AACGC
+4075_3_12	AACGC
+4075_3_2	AACGC
+4075_3_3	AACGC
+4075_3_5	AACGC
+4075_3_6	AACGC
+4075_3_7	AACGC
+4075_3_8	AACGC
+4075_3_9	AACGC
+4370_2_11	AACGC
+4370_2_12	AACGC
+4370_2_2	AACGC
+4370_2_3	AACGC
+4370_2_4	AACGC
+4370_2_7	AACGC
+4370_2_8	AACGC
+4370_2_9	AACGC
+4370_3_11	AACGC
+4370_3_1	AACGC
+4370_3_6	AACGC
+4370_3_7	AACGC
+4370_3_8	AACGC
+5174_5_1	GACGC
+5174_5_2	AACGC
+5174_5_3	AACGC
+5174_5_4	AACGC
+5174_5_5	AACGC
+5174_5_6	AACGC
+5174_5_7	GACGC
+5174_5_9	GACGC
+5174_6_10	GACGC
+5174_6_1	AACGC
+5174_6_2	AACGC
+5174_6_3	AACGC
+5174_6_4	AACGC
+5174_6_5	AACGC
+5174_6_6	AACGC
+5174_6_7	AACGC
+5174_6_8	AACGC
+5174_6_9	AACGC
+5174_7_10	AACGC
+5174_7_1	GACGC
+5174_7_2	AACGC
+5174_7_3	AACGC
+5174_7_4	AACGC
+5174_7_5	AACGC
+5174_7_6	AACGC
+5174_7_7	AACGC
+5174_7_8	AACGC
+5174_7_9	AACGC
+5174_8_1	AACGC
+5174_8_2	AACGC
+5174_8_3	AACGC
+5174_8_5	GACGC
+5174_8_6	AACGC
+5174_8_8	AACGC
+5174_8_9	AACGC
+Vibrio_parahaemolyticus	-----
+Vibrio_vulnificus	-GGA-
diff --git a/tests/data/alignment_file_one_line_per_sequence.aln.vcf b/tests/data/alignment_file_one_line_per_sequence.aln.vcf
new file mode 100644
index 0000000..3422500
--- /dev/null
+++ b/tests/data/alignment_file_one_line_per_sequence.aln.vcf
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.1
+##INFO=<ID=AB,Number=1,Type=String,Description="Alt Base">
+#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	824	.	A	G	.	.	AB	.	.	.	.	.	.	.	G	G	.	.	.	G	.	G	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	G	G	G	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	.	.	.	.	G	.	.	.	.	.
+1	1277	.	A	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
+1	1280	.	C	G	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G
+1	1298	.	G	A	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	A
+1	1434	.	C	T	.	.	AB	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.

From 413134df5da76f1af363892257669dbcc7625718 Mon Sep 17 00:00:00 2001
From: andrewjpage <andrewjpage@gmail.com>
Date: Tue, 24 Jan 2012 10:23:46 +0000
Subject: [PATCH 2/2] treat N as gap

---
 alignment_file.c      |   4 ++--
 parse_phylip.c        |   2 +-
 snp_sites             | Bin 23176 -> 23220 bytes
 tests/check_snp_sites | Bin 32376 -> 32420 bytes
 vcf.c                 |   4 ++--
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/alignment_file.c b/alignment_file.c
index bbd8cda..d7a8b44 100644
--- 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
index 62b01c2..898452c 100644
--- 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
index d1099b503950a5280a3dd91347c38a116081d7f1..4e4330fb31e49eab94394e7d3cd22a7ddace08f3 100755
GIT binary patch
delta 4092
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zp=h>D*;&>)IW@MKSbsXx)M#xi{#1=bqY1_t8{09RnxrXa*3J@`$fWDfIK=I_@7;xm
zw&>ga&b{ZJd(OG%-ut%um~ix%u;WmQ-U_fXA3%TP*nCkqir<Ki{AU5+Y9qkFB!DTz
z4fL?Tsr)IW?^>+YID`gVrKvRT|9DIP&g^RmOL@!v{WEUO!$X=`qTY(<H0iyg8sj94
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Mp?71Gh3$s_0$a#?8~^|S

delta 3778
zcmZ{n4^)%a6~N#3CD4FLlRzK|f&764l8_)G$RFcG$5(5s77GGat*yGP*7~nQdvsc~
znP?h9+uc*!^{k4{)8nbyQ<t&fZ0)RVSzV9Xj?UvYH_k?FI<l3OR4dA|`@X!854QpN
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diff --git a/tests/check_snp_sites b/tests/check_snp_sites
index 381f7899f5868b1f415236262a3b49b07e623aef..d82a0ad1ca0b6c43cdafa704443e8ab7005b9d12 100755
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diff --git a/vcf.c b/vcf.c
index a531e03..e28b800 100644
--- 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, "." );	
 		}