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cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
GNU Affero General Public License v3.0
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SV Data Visualisation Error #10372

Open sbabyanusha opened 1 year ago

sbabyanusha commented 1 year ago

Noticed an error regarding the sv data visualisation. https://www.cbioportal.org/results/structuralVariants?cancer_study_list=brca_tcgapan[…]0&tab_index=tab_visualize&Action=Submit&mutations_gene=TP53

Any idea why read counts are -1? We don't have Normal Read Count
Tumor Read Count
Normal Variant Count
Tumor Variant Count Normal Paired-End Read Count
Normal Split Read Count

These are not in our data file at all. But is it showing up as "-1" in the portal?

Screen Shot 2023-09-05 at 4 16 37 PM

Maybe the portal is using -1 as default for columns that are not in the data file?

Screen Shot 2023-09-05 at 4 04 15 PM
alisman commented 11 months ago

@inodb @dippindots @JREastonMarks I looked into this one. -1 is inserted into database on import for numerical columns which do not have any data. This is then being surfaced as -1 in the portal. Should we just handle this on frontend or should these really be null?