Human GRCh37/hg19 turns into all T's

danvk commented 9 years ago

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

dasmoth commented 9 years ago

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 commented 9 years ago

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

dasmoth / dalliance

Human GRCh37/hg19 turns into all T's #104