From 2929c7e31248922372dd8bccc57c56571be275d1 Mon Sep 17 00:00:00 2001 From: Daniel Cameron Date: Tue, 20 Jun 2023 23:04:46 +1000 Subject: [PATCH 1/3] #717 Fixed DP to be parsable as an integer --- test/vcf/4.3/failed/failed_body_format_006.vcf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 test/vcf/4.3/failed/failed_body_format_006.vcf diff --git a/test/vcf/4.3/failed/failed_body_format_006.vcf b/test/vcf/4.3/failed/failed_body_format_006.vcf old mode 100644 new mode 100755 index 55cbc8735..4aec90d1f --- a/test/vcf/4.3/failed/failed_body_format_006.vcf +++ b/test/vcf/4.3/failed/failed_body_format_006.vcf @@ -1,4 +1,4 @@ ##fileformat=VCFv4.3 ##CauseOfFailure=FORMAT predefined tag GT has missing alleles #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 -1 100 rs;rsa C T 100 PASS AB=1 GT:DP:GP 0/|1:12:0,0.1,0 0|1:1.000:0.1,1,0.12 +1 100 rs;rsa C T 100 PASS AB=1 GT:DP:GP 0/|1:12:0,0.1,0 0|1:1:0.1,1,0.12 From dbf3f7b657b57fc53839ffd41ad132e3e0379301 Mon Sep 17 00:00:00 2001 From: Daniel Cameron Date: Wed, 21 Jun 2023 00:33:46 +1000 Subject: [PATCH 2/3] #689 % characters fail the FORMAT regex --- .../passed_body_format.vcf => failed/failed_body_format_007.vcf} | 1 + 1 file changed, 1 insertion(+) rename test/vcf/4.3/{passed/passed_body_format.vcf => failed/failed_body_format_007.vcf} (93%) diff --git a/test/vcf/4.3/passed/passed_body_format.vcf b/test/vcf/4.3/failed/failed_body_format_007.vcf similarity index 93% rename from test/vcf/4.3/passed/passed_body_format.vcf rename to test/vcf/4.3/failed/failed_body_format_007.vcf index db7062fcc..b80c49226 100644 --- a/test/vcf/4.3/passed/passed_body_format.vcf +++ b/test/vcf/4.3/failed/failed_body_format_007.vcf @@ -1,4 +1,5 @@ ##fileformat=VCFv4.3 +##CauseOfFailure=FORMAT regex failure #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 1 100 rs180734498 C T 100 PASS AC=4 GT 0|0 0|1 1 200 rs180734498 C T 100 PASS AC=4 GL -0.13,-0.58,-3.62 -2.45,-0.00,-5.00 From 09a3195a945a1f768098b0152d281603bc487819 Mon Sep 17 00:00:00 2001 From: Daniel Cameron Date: Wed, 21 Jun 2023 00:54:47 +1000 Subject: [PATCH 3/3] Added VCF test cases for reserved integers and under/overflow --- .../4.3/failed/failed_body_info_integer_overflow.vcf | 5 +++++ .../4.3/failed/failed_body_info_integer_reserved.vcf | 12 ++++++++++++ .../failed/failed_body_info_integer_underflow.vcf | 5 +++++ 3 files changed, 22 insertions(+) create mode 100644 test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf create mode 100644 test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf create mode 100644 test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf diff --git a/test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf b/test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf new file mode 100644 index 000000000..0e24e4f88 --- /dev/null +++ b/test/vcf/4.3/failed/failed_body_info_integer_overflow.vcf @@ -0,0 +1,5 @@ +##fileformat=VCFv4.3 +##INFO= +##CauseOfFailure=INFO integer overflow +#CHROM POS ID REF ALT QUAL FILTER INFO +1 123 . C T 100 PASS INT=2147483648 diff --git a/test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf b/test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf new file mode 100644 index 000000000..4c27fef9d --- /dev/null +++ b/test/vcf/4.3/failed/failed_body_info_integer_reserved.vcf @@ -0,0 +1,12 @@ +##fileformat=VCFv4.3 +##INFO= +##CauseOfFailure=INFO integer reserved value +#CHROM POS ID REF ALT QUAL FILTER INFO +1 1 . C T 100 PASS INT=-2147483648 +1 2 . C T 100 PASS INT=-2147483647 +1 3 . C T 100 PASS INT=-2147483646 +1 4 . C T 100 PASS INT=-2147483645 +1 5 . C T 100 PASS INT=-2147483644 +1 6 . C T 100 PASS INT=-2147483643 +1 7 . C T 100 PASS INT=-2147483642 +1 8 . C T 100 PASS INT=-2147483641 diff --git a/test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf b/test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf new file mode 100644 index 000000000..a8eef0ce1 --- /dev/null +++ b/test/vcf/4.3/failed/failed_body_info_integer_underflow.vcf @@ -0,0 +1,5 @@ +##fileformat=VCFv4.3 +##INFO= +##CauseOfFailure=INFO integer overflow +#CHROM POS ID REF ALT QUAL FILTER INFO +1 123 . C T 100 PASS INT=-2147483649