From 347ad584b4b6b088dc812242af7bf29dcc8dc6ef Mon Sep 17 00:00:00 2001 From: James Bonfield Date: Thu, 11 Nov 2021 17:17:16 +0000 Subject: [PATCH] Fix END < POS issue in vcf tests. 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. --- test/vcf/4.3/passed/passed_body_alt.vcf | 6 +++--- test/vcf/4.3/passed/passed_body_info.vcf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/test/vcf/4.3/passed/passed_body_alt.vcf b/test/vcf/4.3/passed/passed_body_alt.vcf index f3d441287..cdd2a96ce 100644 --- a/test/vcf/4.3/passed/passed_body_alt.vcf +++ b/test/vcf/4.3/passed/passed_body_alt.vcf @@ -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 <*>, . . END=4388 GT:DP:GQ 0/0:25:45 0/1:23:99 +1 4389 . C <*>, . . 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 . . END=4390 GT:DP:GQ 0/0:26:0 0/0:25:60 -1 4391 . C . . END=4390 GT:DP:GQ 0/0:26:0 0/0:25:60 +1 4391 . C . . END=4391 GT:DP:GQ 0/0:26:0 0/0:25:60 +1 4391 . C . . END=4391 GT:DP:GQ 0/0:26:0 0/0:25:60 diff --git a/test/vcf/4.3/passed/passed_body_info.vcf b/test/vcf/4.3/passed/passed_body_info.vcf index f358c72aa..240651cb0 100644 --- a/test/vcf/4.3/passed/passed_body_info.vcf +++ b/test/vcf/4.3/passed/passed_body_info.vcf @@ -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