Offset error when entering genomic coordinates between exons

[jarbesfeld]

Describe the bug

A Transcript Segment object is currently not being created when a genomic coordinate that occurs between exons is supplied to start or end.

Steps to reproduce

1. Select Transcript Segment Object, genomic coordinates and transcript
2. For transcript, enter NM_152263.3
3. For chromosome, enter NC_000001.11
4. For ending position, enter 154191900

Expected behavior

We would expect exon 1 to be chosen with an offset of 1

Current behavior

The offset is not appearing in the top right of the object (instead a loading circle shows)

Possible reason(s)

It's possible the code needs to be updated to include the offset calculation when a genomic breakpoint occurs in between exons. This should allow for the correct offset to be computed.

Suggested fix

No response

Branch, commit, and/or version

I was looking at http://fusion-curation-dev-eb.us-east-2.elasticbeanstalk.com/assayed-fusion

Screenshots

No response

Environment details

Mac M1

Additional details

No response

Contribution

None

[jarbesfeld]

I think this would be good to address now, since it's likely that users will have cases where aligned genomic breakpoints occur between exons

[jsstevenson]

I can't remember where we wrote this down, but Alex had at one point suggested some kind of visual warning if you try to put in a coordinate that's more than 50 bp's away from an exon

[korikuzma]

@jarbesfeld says this is the highest priority issue after #311

[katiestahl]

GenomicMedLab/cool-seq-tool#368

[github-actions]

Closed by #336.