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add test for the structural variant case where ref and alt starts wit…
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…h same allele
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nitin-ebi committed Nov 6, 2024
1 parent dcc39c0 commit 72a9bcf
Showing 1 changed file with 4 additions and 4 deletions.
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Expand Up @@ -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
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