Ino de Bruijn comments

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                                            Ino de Bruijn

Filter studies by reference genome

@BasLee one more question: is there a use case to be able to select both hg19 + hg38? If not it might be cleaner to just list in the examples:...

Filter studies by reference genome

Thanks @BasLee ! Looks like there's still an issue vs production for queries not part of example queries: PR: ![Screen Shot 2022-09-16 at 10 44 03 AM](https://user-images.githubusercontent.com/1334004/190666244-3e4e260b-a8d8-431f-8900-9aad2cf01519.png) Production: ![Screen Shot...

strange behavior for gene validator

There are many genes with duplicate symbols: https://docs.google.com/spreadsheets/d/1faa6pufHkwlFFNhSOIE4X-c8Z-rrB2GJof7L_QviXOs/edit#gid=0. We can try to manually replace maybe some as a temp fix while @rmadupuri et al continue the switch to HGNC effort

cBioPortal Data Collection Automation

@ao508 I noticed this was transferred from GSoC. If we are not working on it, maybe we can transfer it back?

failed gsva tests

Implement annotation filtering for new structural variants

@alisman yes should be listed

Issues with alteration frequency and profiled cases counting in the backend

> 2. Calculated frequencies for certain genes are most likely incorrect now. We should probably display `N/A`, or just hide these genes when the number of profiled cases happens to...

Generalize Indexing for Session Service

Structural variant data not always displaying on MSK cBioPortal and inconsistent with public site

Thanks for reporting @karissawhiting ! - @dippindots is looking at the first issue (SV data missing from [MSK portal](https://www.cbioportal.org/study/summary?id=blca_nmibc_2017)) - @sbabyanusha is looking at reimporting the studies you mentioned into...

Circleci performance improvement

@rmadupuri good point! @dippindots it should be possible to redirect the output if you add some statement like `> myjob_output.txt`. Then at the end you could either show the output...