Integer overflow with bigwig files

[enuggetry]

http://gmod.827538.n3.nabble.com/Gmod-ajax-Integer-overflow-with-bigwig-files-td4051345.html

A thread that is now getting pretty old from last year is still biting me (or biting me again, as I set it aside last year to work on other things) is here:

http://gmod.827538.n3.nabble.com/Gmod-ajax-integer-overflow-error-in-Jbrowse-td4039019.html

An example of this problem can be seen here (for me at least):

http://staging.wormbase.org/tools/genome/jbrowse/full.html?data=data%2Fc_elegans_PRJNA13758&loc=II%3A9897349..9900127&tracks=TSS%20(Chen)%20Forward&highlight=

When I follow that link in any of my browsers, I get a pink box with a message that there was an integer overflow error. Does anybody have any insight into what might be causing that?

In the archived thread, there was mention of clearing caches as well as interactions with proxies, but neither of those is the case in this example.

Thanks,
Scott

[enuggetry]

I'm seeing the problem on Safari 9 and Firefox. The problem does not seem to exhibit on Chrome.

Safari 9 - El Captain

Chrome v45 Win 8.1

[keiranmraine]

Hi,

Grasping at straws but 64 vs 32 bit? Safari and Firefox have an option (certainly on mac) to switch between modes, chrome always opens as 64-bit from what I can tell (assuming 64-bit version):

http://support.slingbox.com/KB/KB-1000319

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

kr2@sanger.ac.uk
Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 25 Sep 2015, at 00:03, enuggetry notifications@github.com wrote:

I'm seeing the problem on Safari 9 and Firefox. The problem does not seem to exhibit on Chrome.

Safari 9 - El Captain

Chrome v45 Win 8.1

—
Reply to this email directly or view it on GitHub.

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office is 215 Euston Road, London, NW1 2BE.

[cmdcolin]

I'm pretty sure the server setup has at least something to do with it. If I setup the whoel thing locally, download assembly and add the bigwig, it works fine.

I mentioned this in the old thread too http://gmod.827538.n3.nabble.com/Gmod-ajax-integer-overflow-error-in-Jbrowse-td4039019.html

I just downloaded a genome assembly from the wormbase site and loaded the given bigwig file and it works fine.

The issue seems to be that, for example in firefox, the entire file is being returned, and it is doing HTTP 200 GET instead of HTTP 206 Partial request chunks of it.

See

[cmdcolin]

Appears Scott resolved the issue by just not using nginx proxying http://gmod.827538.n3.nabble.com/Gmod-ajax-Integer-overflow-with-bigwig-files-td4051345.html

Might want to see why the nginx proxying fails in the first place though

Apache proxying works fine for us 👍

[dkarjala]

Hi,

I am also facing the same issue. In my case I am setting the 206 status.

I am using grails controller to send the bw files from server. I am also setting all the required headers in the response.

Thanks,
Dileep

[nathandunn]

WRT to the 206 case . . Are the TCGA_case_disease_track tracks BW or VCF?

We are currently serving BW out of grails without a problem in one of our branches without incident, but we may not be in the right conditions:

https://github.com/GMOD/Apollo/blob/feature/genometry1/grails-app/controllers/org/bbop/apollo/BigwigController.groovy#L92-L107

The 206 should be normal when reading a byte range.

WRT to the overflow bug . . looks like issued here?:

https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Model/DataView.js#L40

Is this consistent across scaffolds or only for the larger ones?

[cmdcolin]

The "overflow bug" as we have seen here is probably a red herring for something else going on, not genome size related.

Also, the code that you link to @nathandunn is doing extra processing of bigwig files. If you are not doing any processing, you can just do a passthough of the chunks.

It's true that in webapollo we also use grails to serve up bigwigs and other things too. We use code adopted from this "FileServlet" which just passes through binary files and handles 206 range requests http://balusc.omnifaces.org/2007/07/fileservlet.html

[cmdcolin]

Actually i think it is an enhanced version of that fileservlet http://balusc.omnifaces.org/2009/02/fileservlet-supporting-resume-and.html

[dkarjala]

Hi Colin Diesh,

Thanks for the help. I am able to render the bw tracks with the following code http://balusc.omnifaces.org/2009/02/fileservlet-supporting-resume-and.html.

[cmdcolin]

Good to know! I think this can be closed 👍