[Gmod-ajax] multiple tracks with same data file

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[Gmod-ajax] multiple tracks with same data file

Keiran Raine
Hi,

I seems to remember reading somewhere that JBrowse supports a method where you can specify the source of the data for a track so that it can be reused in multiple tracks.

For example Alignments2 and SNPCoverage both reference the same BAM file but I have to defined the storeClass and urlTemplate (and common metadata) multiple times.  Although this is pretty minimal I'm guessing on very large configurations this could have an impact.

So I have 2 questions really:
1. Am I mistaken and I've made this up?
2. Will JBrowse account for the index file being the same or download it twice?

Thanks

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 Rese arch 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: multiple tracks with same data file

Robert Buels-2
Yes, it supports this.  You can write your configuration like:

   tracks: [
     { label: 'alignments', type: 'Alignments2',
       store: 'store12345'
     },
     { label: 'coverage', type: 'SNPCoverage',
       store: 'store12345'
     }
   ],
   stores: {
      store12345: {
          type: 'BAM',
          urlTemplate: 'alignments.bam'
      }
   }

This format isn't promulgated on the wiki or in tutorials, because it
isn't backward-compatible with older versions of JBrowse.

Even if you don't do this, the caching that the browser does, combined
with a global cache of byte ranges maintained by JBrowse itself, will
mostly prevent resources and ranges thereof being fetched multiple times.

However, separating your store configurations like this is good for
maintainability and for making sure all of JBrowse's various caching
mechanisms are being used to full effect.


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

On 10/25/2013 09:33 AM, Keiran Raine wrote:

> Hi,
>
> I seems to remember reading somewhere that JBrowse supports a method
> where you can specify the source of the data for a track so that it can
> be reused in multiple tracks.
>
> For example Alignments2 and SNPCoverage both reference the same BAM file
> but I have to defined the storeClass and urlTemplate (and common
> metadata) multiple times.  Although this is pretty minimal I'm guessing
> on very large configurations this could have an impact.
>
> So I have 2 questions really:
> 1. Am I mistaken and I've made this up?
> 2. Will JBrowse account for the index file being the same or download it
> twice?
>
> Thanks
>
> 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 Rese arch
> 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.
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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