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populationgenomics / seqr

web-based analysis tool for rare disease genomics
GNU Affero General Public License v3.0
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Update IGV version #21

Open illusional opened 3 years ago

illusional commented 3 years ago

From @lgruen (just creating a placeholder issue):

It might be worth trying to update the IGV.js version. If I understand correctly, the currently used version is 2.2.2 (https://github.com/populationgenomics/seqr/blob/dev/ui/package-lock.json#L10159), which is from January 2019.

Fetching the CRAM ranges is implemented as a call to gsutil (e.g. gsutil cat -r 655360-688127 gs://cpg-seqr-testing/NA12878_trio/NA12878.cram). That could probably be sped up a bit too, but the main issue seems to be the large number of range requests that get queued (about a 100 for a single view).

lgruen commented 3 years ago

I think #34 might have broken seqr in a weird way for me and I wonder whether this is reproducible for others. IGV.js never finishes loading the Refseq Genes track for me and just keeps burning CPU while the window stays unresponsive.

Steps to reproduce:

  1. Navigate to https://seqr-dev.populationgenomics.org.au/variant_search/results/c9aa973a576ca2decefe9719254b0e52?page=1&sort=xpos.
  2. Click on "show reads" for the first AP006222.2 variant.

Here's a video of the behavior: https://drive.google.com/file/d/1rqbtuNNn557r8sxpdkdn975AQ4WAhEgi/view?usp=sharing