From 72a9bcf14232a30912a25bfa308b464cf73788de Mon Sep 17 00:00:00 2001 From: nkumar2 Date: Wed, 6 Nov 2024 13:30:47 +0000 Subject: [PATCH] add test for the structural variant case where ref and alt starts with same allele --- .../jobs/steps/GenotypedVcfTestSkipStructuralVariant.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/test/java/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/GenotypedVcfTestSkipStructuralVariant.java b/src/test/java/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/GenotypedVcfTestSkipStructuralVariant.java index 6cacb644..826e1f9a 100644 --- a/src/test/java/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/GenotypedVcfTestSkipStructuralVariant.java +++ b/src/test/java/uk/ac/ebi/eva/pipeline/configuration/jobs/steps/GenotypedVcfTestSkipStructuralVariant.java @@ -75,17 +75,17 @@ public void loaderStepShouldSkipStructuralVariants() throws Exception { } /* - * This test case represent a special case of structural variants that should be skipped, but due to a bug makes it's + * This test case represents a special case of structural variants that should be skipped, but due to a bug makes its * way into the DB. * * The variant has ref as "G" and alt as "G[2:421681[", which means it fits the definition of a structural variant * and should be skipped by the variant processor that filters out structural variants. * * But instead what is currently happening is that after the variant is read, the normalization process in variant - * reader removes the prefix G and the variant is eventually reduced to ref "" and alt "[2:421681[", which does get - * parsed correctly by the regex in @ExcludeStructuralVariantsProcessor and makes it's way into the DB. + * reader removes the prefix G and the variant is eventually reduced to ref "" and alt "[2:421681[", which does not get + * parsed correctly by the regex in @ExcludeStructuralVariantsProcessor and makes its way into the DB. * - * Currently, the test case fails and that's why we are skipping it for now. It should start passing once we have fixed the + * Currently, the test case fails therefore we are skipping it for now. It should start passing once we have fixed the * problem with the normalization in the variant reader. */ @Ignore