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Published 20 hours ago • verified publisher icon dasmoth

Human GRCh37/hg19 turns into all T's

Open danvk opened this issue 11 years ago • 2 comments

To reproduce:

  • Visit http://www.biodalliance.org/human37.html
  • Type in "20:2,684,623..2,684,723" and hit enter to zoom to that part of chr20
  • Click & drag to scroll to the left.

Eventually you get to a region of all T's. IGV does not have such a region, and the pileups below also indicate that it's incorrect.

reference ts

danvk avatar Sep 22 '14 23:09 danvk

Am I right in thinking that this is Chrome? I could reproduce in Chrome but not in Firefox.

I'm pretty certain there isn't a logic bug in the Dalliance .2bit fetching code -- instead, it's getting a bunch of zeroes back from a legitimate HTTP request. I suspect that this might be a bug in Chrome, most likely related to how results of partial (Range) requests get cached. I'll see if I can distill it down into something that can be submitted as a Chrome/Blink bug.

For now, I've made a small change which should prevent cached resources being used when fetching sequence. This will be included in the 0.12.8 and 0.13 releases unless we can come up with a better answer!

dasmoth avatar Sep 23 '14 08:09 dasmoth

Chrome bug filed: https://code.google.com/p/chromium/issues/detail?id=416895

dasmoth avatar Sep 23 '14 16:09 dasmoth