Skip to content

Commit

Permalink
Remove blank line from a vcf test file (#606)
Browse files Browse the repository at this point in the history 
* Remove blank line from vcf test files

* Fix END < POS issue in vcf tests. (PR#606)

This was clarified in 035946a as illegal.

Fixes #607, although for added clarity we may wish to have a follow up
PR to amend the BCF parts of the specification to use unsigned data
types when the values are infact only permitted to be unsigned.
  • Loading branch information
@jkbonfield
jkbonfield authored Apr 19, 2022
1 parent 7922706 commit 0c0acb3
Show file tree
Hide file tree
Showing 7 changed files with 6 additions and 9 deletions.
2 changes: 1 addition & 1 deletion test/vcf/4.1/passed/passed_body_info.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
6 300 rs180734498 C T 100 PASS DB=1 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 100 rs180734498 C T 100 PASS DP=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 200 rs180734498 C T 100 PASS DP=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=100 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 200 rs180734498 C T 100 PASS END=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 100 rs180734498 C T 100 PASS H2 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 200 rs180734498 C T 100 PASS H2=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
Expand Down
1 change: 0 additions & 1 deletion test/vcf/4.1/passed/passed_meta_pedigree.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,3 @@
##PEDIGREE=<Name_0=Something,Name_1=Something_else,Name_2=Something.more>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 123 . TC T . . .

2 changes: 1 addition & 1 deletion test/vcf/4.2/passed/passed_body_info.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
6 300 rs180734498 C T 100 PASS DB=1 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 100 rs180734498 C T 100 PASS DP=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 200 rs180734498 C T 100 PASS DP=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=100 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 200 rs180734498 C T 100 PASS END=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 100 rs180734498 C T 100 PASS H2 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 200 rs180734498 C T 100 PASS H2=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
Expand Down
1 change: 0 additions & 1 deletion test/vcf/4.2/passed/passed_meta_pedigree.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,3 @@
##PEDIGREE=<Name_0=Something,Name_1=Something_else,Name_2=Something.more>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 123 . TC T . . .

6 changes: 3 additions & 3 deletions test/vcf/4.3/passed/passed_body_alt.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@
1 1900 rs180734498 C . 100 PASS AN=2184;AC=249;AF=0.11 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
1 4370 . G <*> . . END=4383 GT:DP:GQ:MIN:PL 0/0:25:60:23:0,60,900 0/0:25:45:25:0,42,630
1 4389 . T TC,<*> 213.73 . . GT:DP:GQ:PL 0/1:23:99:51,0,36,93,92,86 0/0:24:52:0,52,95,66,95,97
1 4389 . C <*>,<DEL> . . END=4388 GT:DP:GQ 0/0:25:45 0/1:23:99
1 4389 . C <*>,<DEL> . . END=4389 GT:DP:GQ 0/0:25:45 0/1:23:99
1 4390 . C *,<*> . . END=4390 GT:DP:GQ 0/0:26:0 0/0:25:60
1 4391 . C <UNK> . . END=4390 GT:DP:GQ 0/0:26:0 0/0:25:60
1 4391 . C <validIdWithSymbols!"#$%&'()*+-./;=?@[\]^_`{|}~> . . END=4390 GT:DP:GQ 0/0:26:0 0/0:25:60
1 4391 . C <UNK> . . END=4391 GT:DP:GQ 0/0:26:0 0/0:25:60
1 4391 . C <validIdWithSymbols!"#$%&'()*+-./;=?@[\]^_`{|}~> . . END=4391 GT:DP:GQ 0/0:26:0 0/0:25:60
2 changes: 1 addition & 1 deletion test/vcf/4.3/passed/passed_body_info.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
6 300 rs180734498 C T 100 PASS DB=1 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 100 rs180734498 C T 100 PASS DP=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
7 200 rs180734498 C T 100 PASS DP=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 100 rs180734498 C T 100 PASS END=100 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
8 200 rs180734498 C T 100 PASS END=2184 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 100 rs180734498 C T 100 PASS H2 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
9 200 rs180734498 C T 100 PASS H2=0 GT:DS:GL 0|0:0.050:-0.13,-0.58,-3.62 0|1:1.000:-2.45,-0.00,-5.00
Expand Down
1 change: 0 additions & 1 deletion test/vcf/4.3/passed/passed_meta_pedigree.vcf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,3 @@
##PEDIGREE=<ID=SampleID,Name_1=Ancestor_1,Name_2=Ancestor_2,Name_3=Ancestor3>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 123 . TC T . . .

0 comments on commit 0c0acb3

Please sign in to comment.