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Fix END < POS issue in vcf tests. (PR#606)
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This was clarified in 035946a as illegal.

Fixes samtools#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.
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@jkbonfield
jkbonfield committed Feb 2, 2022
1 parent 83fa45d commit f1aedd7
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Showing 4 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion test/vcf/4.1/passed/passed_body_info.vcf
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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
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2 changes: 1 addition & 1 deletion test/vcf/4.2/passed/passed_body_info.vcf
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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
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6 changes: 3 additions & 3 deletions test/vcf/4.3/passed/passed_body_alt.vcf
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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
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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
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