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Incorrect representation when CDS has no parent exon #428

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dariober opened this issue Aug 27, 2024 · 0 comments
Open

Incorrect representation when CDS has no parent exon #428

dariober opened this issue Aug 27, 2024 · 0 comments

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@dariober
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In commit 22db7bd CDSs without parent exons are incorrectly represented. Consider gene02 from packages/jbrowse-plugin-apollo/test_data/cdsChecks/stopcodon.gff3:

chr2	.	gene	1	30	.	+	.	ID=gene02
chr2	.	mRNA	1	30	.	+	.	ID=mrna02;Parent=gene02
chr2	.	CDS	1	9	.	+	0	ID=cds02.1;Parent=mrna02
chr2	.	CDS	16	30	.	+	0	ID=cds02.2;Parent=mrna02

It should have two CDSs, but instead is:

image

gene03 has the same structure but it includes exons and it looks fine:

chr3	.	gene	1	30	.	+	.	ID=gene03
chr3	.	mRNA	1	30	.	+	.	ID=mrna03;Parent=gene03
chr3	.	exon	1	9	.	+	0	Parent=mrna03
chr3	.	exon	16	30	.	+	0	Parent=mrna03
chr3	.	CDS	1	9	.	+	0	ID=cds03;Parent=mrna03
chr3	.	CDS	16	30	.	+	0	ID=cds03;Parent=mrna03

image

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