search

Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
148 stars 45 forks source link

Opening IGV on a repeat region sometimes causes the view to crash or stall #1783

Closed northwestwitch closed 7 months ago

northwestwitch commented 4 years ago

Sometimes (could be related when read mate is on another chromosome?) when clicking on a "view mate in split screen" causes the views to crash.

Possibly a javascript error. Make sure to check what the browser page "inspect" options says about it

dnil commented 4 years ago

Any connection to what chr the mate is on?

northwestwitch commented 4 years ago

Any connection to what chr the mate is on?

Chr2? It's not even a weird one!

dnil commented 4 years ago

Is it reproducible, transient or intermittent?

northwestwitch commented 4 years ago

Reproducible I think. Case example: cust010, case A1539 igv interval chr12:110021000-110021100.

dnil commented 4 years ago

So I wasn't able to crash the browser, but I did note that many reads there go to mates in loooong polyG homopolymer stretches. It is perhaps not so strange to find an issue with those. If you can pinpoint the exact reads that fail, maybe we can see if the issue is with the split screen, the other region or the tags on that particular read?

northwestwitch commented 4 years ago

No you are right, I didn't express myself well. The browser doesn't crash but freezes while trying to load the reads. Is this what you saw?

dnil commented 4 years ago

Yep; moving around in deep ambiguous repeats is not the best sport of the regular IGV either. Possibly we could do something with samplingDepthand samplingWindowSize?

dnil commented 4 years ago

If it is a bug, I'd lean towards it being in igv.js? We could mitigate however, but relabelling for now.

dnil commented 7 months ago

Several versions of IGV.js have passed; while I am not sure all slowness issues with deep alignments are fixed, I think we can close this and reopen with a current example when we have one.