Fix import of structural variants from query into oncoprinter #4091
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
dippindots
requested changes
Dec 16, 2021
There was a problem hiding this comment.
@adamabeshouse The unit tests are failing, it looks like there are some tests need to be updated, besides that, this looks good to me.
alisman
reviewed
Dec 16, 2021
| @@ -142,7 +143,8 @@ function getOncoprinterGeneticInputLine(parsed: OncoprinterGeneticInputLine) { | |||
| line.push('PROT'); | |||
| break; | |||
| case AlterationTypeConstants.STRUCTURAL_VARIANT: | |||
| line.push('STRUCTURAL VARIANT'); | |||
| line.push(parsed.eventInfo || 'structural_variant'); | |||
There was a problem hiding this comment.
maybe comment why it would be missing eventInfo?
There was a problem hiding this comment.
I just wanted to do this as a catch in case there's missing data. would eventInfo always exist for structural variants?
alisman
approved these changes
Dec 16, 2021
Signed-off-by: Adam Abeshouse <abeshoua@mskcc.org>
adamabeshouse
force-pushed
the
9068-sv-oncoprinter
branch
from
9be1375
to
ac0450e
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes cBioPortal/cbioportal#9068
it's not perfect, as I still need to implement oncokb annotation of structural variants in oncoprinter. But that is a bit more work because it requires additional user input of the site1 and site2 genes.