<DEL> in alt field leads to crossed out entry in table

igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

MIT License

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<DEL> in alt field leads to crossed out entry in table #15

Closed johanneskoester closed 3 years ago

johanneskoester commented 5 years ago

When a VCF file contains a <DEL> allele, the corresponding entry in the HTML table is not rendered correctly. Seems like the <DEL> is interpreted as HTML tag. I suggest to escape all VCF entries before rendering them in the table.

igv-report-del-bug

jrobinso commented 5 years ago

Thanks for the report. This is still in beta test phase, I'm interested to learn more about how its being used if you care to share.

johanneskoester commented 5 years ago

Sure. I am evaluating the use in a personalized medicine pipeline, where tumor somatic variants are called on patient data.

jrobinso commented 5 years ago

Good to know, that's just the sort of application I had in mind. I'll attend to this later today.