From e2da3098e94964d0d4a9b695c9fdff5e2fc5fb51 Mon Sep 17 00:00:00 2001 From: Ben Taylor Date: Thu, 3 Sep 2015 09:52:09 +0000 Subject: [PATCH 1/2] Remove a rogue tab from header line Some tools don't like a VCF header ending with a tab. The spec is ambiguous --- src/vcf.c | 4 ++-- tests/data/alignment_file_one_line_per_sequence.aln.vcf | 2 +- tests/data/alignment_file_with_n.aln.vcf | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/vcf.c b/src/vcf.c index b977795..488a0ed 100644 --- a/src/vcf.c +++ b/src/vcf.c @@ -57,11 +57,11 @@ void output_vcf_header( FILE * vcf_file_pointer, char ** sequence_names, int num fprintf( vcf_file_pointer, "##fileformat=VCFv4.1\n" ); fprintf( vcf_file_pointer, "##contig=\n", length_of_genome ); fprintf( vcf_file_pointer, "##FORMAT=\n" ); - fprintf( vcf_file_pointer, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" ); + fprintf( vcf_file_pointer, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" ); for(i=0; i ##FORMAT= -#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 +#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 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 diff --git a/tests/data/alignment_file_with_n.aln.vcf b/tests/data/alignment_file_with_n.aln.vcf index a32415d..3186cc0 100644 --- a/tests/data/alignment_file_with_n.aln.vcf +++ b/tests/data/alignment_file_with_n.aln.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.1 ##contig= ##FORMAT= -#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 +#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 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 From 965d311cd9a794d84325bcd31c0d6d33d0e75617 Mon Sep 17 00:00:00 2001 From: Ben Taylor Date: Thu, 3 Sep 2015 09:54:26 +0000 Subject: [PATCH 2/2] Bump patch version to 2.0.2 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 38f77a6..e9307ca 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.0.1 +2.0.2