Merge pull request #22 from sanger-pathogens/BT5_remove_tab

Remove a tab in VCF header
sanger-pathogens · Sep 3, 2015 · 9304a6e · 9304a6e
2 parents 2137cdf + 965d311
commit 9304a6e
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.0.1
+2.0.2
diff --git 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=<ID=1,length=%i>\n", length_of_genome ); 
  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" );
+ fprintf( vcf_file_pointer, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT" );
 
  for(i=0; i<number_of_samples; i++)
  {
- fprintf( vcf_file_pointer, "%s\t", sequence_names[i]);
+ fprintf( vcf_file_pointer, "\t%s", sequence_names[i]);
  }
  fprintf( vcf_file_pointer, "\n");
 }

diff --git a/tests/data/alignment_file_one_line_per_sequence.aln.vcf b/tests/data/alignment_file_one_line_per_sequence.aln.vcf
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##contig=<ID=1,length=2000>
 ##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 
+#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
@@ -1,7 +1,7 @@
 ##fileformat=VCFv4.1
 ##contig=<ID=1,length=2000>
 ##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 
+#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