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Add integration tests in Funcotator for out of bounds variants #7523

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jonn-smith opened this issue Oct 25, 2021 · 0 comments
Open

Add integration tests in Funcotator for out of bounds variants #7523

jonn-smith opened this issue Oct 25, 2021 · 0 comments

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@jonn-smith
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Add more test cases for the errors seen in issue #6289

Specifically we should add both more unit tests and integration tests.

One variant that should be added in integration tests is the following:

##fileformat=VCFv4.1
##contig=<ID=chr9,length=138394717>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample
chr9	67726241	.	TCA	TCACACA,TCACACACA	182	PASS	.	GT	./.

The issue with adding more tests is that we don't have the full Funcotator datasources in our git-lfs repo because of size concerns. To add tests we'll need to add more intervals to our datasources to support the variants' loci, or create variants in the regions we already cover.

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