[Gmod-ajax] chunkSizeLimit: different limit for specific chromosome?

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[Gmod-ajax] chunkSizeLimit: different limit for specific chromosome?

Keiran Raine
Hi Robert,

Is it possible to specify a multiplier for chunkSizeLimit for a particular chromosome?  Generally the default is fine but for mitochondria the default value isn't even big enough for 96bp, nor BW histogram.

Realistically this is probably inly an issue for MT.

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: chunkSizeLimit: different limit for specific chromosome?

Robert Buels-2
Ah.  Actually, what I probably need to do is have the CanvasFeatures
code try to switch to histograms if it hits the chunksizelimit (which is
actually a thrown JBrowse.Errors.DataOverflow error internally).

It's not doing that right now.

Doesn't that seem like the best course?

Anyway, the chunkSizeLimit is there because browsers start to choke when
chunks of BAM files are very big.  A line has to be drawn somewhere.
But, if you up the limit and things seem to be OK, it shouldn't have any
ill effects on the other reference sequences, so I don't think doing it
on a per-refseq basis is really necessary.


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

On 01/03/2014 04:55 PM, Keiran Raine wrote:

> Hi Robert,
>
> Is it possible to specify a multiplier for chunkSizeLimit for a
> particular chromosome?  Generally the default is fine but for
> mitochondria the default value isn't even big enough for 96bp, nor BW
> histogram.
>
> Realistically this is probably inly an issue for MT.
>
> 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: chunkSizeLimit: different limit for specific chromosome?

Keiran Raine
On 3 Jan 2014, at 22:12, Robert Buels <[hidden email]> wrote:

> Ah.  Actually, what I probably need to do is have the CanvasFeatures code try to switch to histograms if it hits the chunksizelimit (which is actually a thrown JBrowse.Errors.DataOverflow error internally).
>
> It's not doing that right now.
>
> Doesn't that seem like the best course?

Yes that would be great, then the user will at least see something.

>
> Anyway, the chunkSizeLimit is there because browsers start to choke when chunks of BAM files are very big.  A line has to be drawn somewhere. But, if you up the limit and things seem to be OK, it shouldn't have any ill effects on the other reference sequences, so I don't think doing it on a per-refseq basis is really necessary.

Probably correct, if the user really want's to see the reads I can explain how to modify the chunkSizeLimit in the interface.

>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 01/03/2014 04:55 PM, Keiran Raine wrote:
>> Hi Robert,
>>
>> Is it possible to specify a multiplier for chunkSizeLimit for a
>> particular chromosome?  Generally the default is fine but for
>> mitochondria the default value isn't even big enough for 96bp, nor BW
>> histogram.
>>
>> Realistically this is probably inly an issue for MT.
>>
>> 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
>>



--
 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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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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