[Gmod-ajax] BAM tracks don't support uncompressed BAM

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[Gmod-ajax] BAM tracks don't support uncompressed BAM

Keiran Raine
Hi Robert,

I've discovered after much digging that one of the tools we are using generates uncompressed BAM files by default.  Although I'm going to correct them it's probably a good idea to:

  • Update the error message to something to help diagnose the problem:
    • currently: 'ReferenceError: end is not defined'.
  • Add support with warning to console that data is uncompressed.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: BAM tracks don't support uncompressed BAM

Robert Buels-2
OK, I'll try to make this better in 1.11.1.

https://github.com/GMOD/jbrowse/issues/404


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 05:47 AM, Keiran Raine wrote:

> Hi Robert,
>
> I've discovered after much digging that one of the tools we are using
> generates uncompressed BAM files by default.  Although I'm going to
> correct them it's probably a good idea to:
>
>   * Update the error message to something to help diagnose the problem:
>       o currently: 'ReferenceError: end is not defined'.
>   * Add support with warning to console that data is uncompressed.
>
>
> Regards,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: BAM tracks don't support uncompressed BAM

Robert Buels-2
In reply to this post by Keiran Raine
Hi Keiran,

I just did some testing on the volvox example bam file like:

gunzip -c volvox-sorted.bam > foo
mv foo volvox-sorted.bam

And the error message that JBrowse gives on that is "Not a BAM file",
which I think is kind of reasonable.

Do you have a sample of your uncompressed BAM output (with a .bai) that
I can try to reproduce this with?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/03/2014 05:47 AM, Keiran Raine wrote:
> ols we are using generates uncompressed BAM files by default.  Although
> I'm going to correct them it's probably a good idea to:

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