[Gmod-ajax] Control when BAM switches to histogram (bw)

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[Gmod-ajax] Control when BAM switches to histogram (bw)

Keiran Raine
Hi,

Can I define the point that the switch between the BAM Alignment2 and the new BW histogram option?  I've got the example from the sample dataset but I don't see an option for this.  I want to define 10,000 bp as the max region for Alignment2 and to be the point that we switch to histogram.

Apologies if this has been answered over the last couple of weeks and I've missed it in the stack of emails.

Thanks, and happy new year to all,

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: Control when BAM switches to histogram (bw)

Robert Buels-2
Sorry for the slow response, I've been on vacation.

It tries to switch over to the histograms when it stops displaying the
individual features, and that is controlled by `maxFeatureScreenDensity`
(which applies to CanvasFeature tracks also, although I just noticed
that it isn't listed on CanvasFeature's conf variable list on the wiki.
  Fixed that just now). See
http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options

maxFeatureScreenDensity is number of features per screen pixel, measured
horizontally.  It defaults to 1 in CanvasFeatures tracks, or 1.5 in
Alignments2 tracks.


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

On 12/31/2013 11:32 AM, Keiran Raine wrote:

> Hi,
>
> Can I define the point that the switch between the BAM Alignment2 and
> the new BW histogram option?  I've got the example
> <https://github.com/GMOD/jbrowse/blob/90debb6fc14066b55d7f7464124cd2fe802eeab6/docs/tutorial/data_files/volvox-sorted.bam.conf#L7> from
> the sample dataset but I don't see an option for this.  I want to define
> 10,000 bp as the max region for Alignment2 and to be the point that we
> switch to histogram.
>
> Apologies if this has been answered over the last couple of weeks and
> I've missed it in the stack of emails.
>
> Thanks, and happy new year to all,
>
> 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: Control when BAM switches to histogram (bw)

Keiran Raine
Hi Robert,

Would it be feasible to add a definite value at some point?

I'm asking as I know I'll get lots of 'bug reports' from our scientists when looking at somatic/comparative data if the BAM track for one sample is in histogram and the other is still showing reads.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 2 Jan 2014, at 05:43, Robert Buels <[hidden email]> wrote:

Sorry for the slow response, I've been on vacation.

It tries to switch over to the histograms when it stops displaying the individual features, and that is controlled by `maxFeatureScreenDensity` (which applies to CanvasFeature tracks also, although I just noticed that it isn't listed on CanvasFeature's conf variable list on the wiki.  Fixed that just now). See http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options

maxFeatureScreenDensity is number of features per screen pixel, measured horizontally.  It defaults to 1 in CanvasFeatures tracks, or 1.5 in Alignments2 tracks.


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

On 12/31/2013 11:32 AM, Keiran Raine wrote:
Hi,

Can I define the point that the switch between the BAM Alignment2 and
the new BW histogram option?  I've got the example
<https://github.com/GMOD/jbrowse/blob/90debb6fc14066b55d7f7464124cd2fe802eeab6/docs/tutorial/data_files/volvox-sorted.bam.conf#L7> from
the sample dataset but I don't see an option for this.  I want to define
10,000 bp as the max region for Alignment2 and to be the point that we
switch to histogram.

Apologies if this has been answered over the last couple of weeks and
I've missed it in the stack of emails.

Thanks, and happy new year to all,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

[hidden email] <[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.


------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
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Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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-- 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: Control when BAM switches to histogram (bw)

Robert Buels-2
You can actually set style.featureScale just like on HTMLFeatures
tracks.  It overrides maxFeatureScreenDensity.




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

On 01/02/2014 04:36 AM, Keiran Raine wrote:

> Hi Robert,
>
> Would it be feasible to add a definite value at some point?
>
> I'm asking as I know I'll get lots of 'bug reports' from our scientists
> when looking at somatic/comparative data if the BAM track for one sample
> is in histogram and the other is still showing reads.
>
> 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
>
> On 2 Jan 2014, at 05:43, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Sorry for the slow response, I've been on vacation.
>>
>> It tries to switch over to the histograms when it stops displaying the
>> individual features, and that is controlled by
>> `maxFeatureScreenDensity` (which applies to CanvasFeature tracks also,
>> although I just noticed that it isn't listed on CanvasFeature's conf
>> variable list on the wiki.  Fixed that just now). See
>> http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options
>>
>> maxFeatureScreenDensity is number of features per screen pixel,
>> measured horizontally.  It defaults to 1 in CanvasFeatures tracks, or
>> 1.5 in Alignments2 tracks.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 12/31/2013 11:32 AM, Keiran Raine wrote:
>>> Hi,
>>>
>>> Can I define the point that the switch between the BAM Alignment2 and
>>> the new BW histogram option?  I've got the example
>>> <https://github.com/GMOD/jbrowse/blob/90debb6fc14066b55d7f7464124cd2fe802eeab6/docs/tutorial/data_files/volvox-sorted.bam.conf#L7>
>>> from
>>> the sample dataset but I don't see an option for this.  I want to define
>>> 10,000 bp as the max region for Alignment2 and to be the point that we
>>> switch to histogram.
>>>
>>> Apologies if this has been answered over the last couple of weeks and
>>> I've missed it in the stack of emails.
>>>
>>> Thanks, and happy new year to all,
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> [hidden email] <mailto:[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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Re: Control when BAM switches to histogram (bw)

Robert Buels-2
In reply to this post by Keiran Raine
You can actually set style.featureScale just like on HTMLFeatures
tracks.  It overrides maxFeatureScreenDensity.  It was missing from the
CanvasFeatures options list, but I just added it.

 From the wiki:

style→featureScale Minimum zoom scale (pixels/basepair) for displaying
individual features in the track. Not set by default, and overrides the
maxFeatureScreenDensity.

Does that do what you need?

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

On 01/02/2014 04:36 AM, Keiran Raine wrote:

> Hi Robert,
>
> Would it be feasible to add a definite value at some point?
>
> I'm asking as I know I'll get lots of 'bug reports' from our scientists
> when looking at somatic/comparative data if the BAM track for one sample
> is in histogram and the other is still showing reads.
>
> 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
>
> On 2 Jan 2014, at 05:43, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> Sorry for the slow response, I've been on vacation.
>>
>> It tries to switch over to the histograms when it stops displaying the
>> individual features, and that is controlled by
>> `maxFeatureScreenDensity` (which applies to CanvasFeature tracks also,
>> although I just noticed that it isn't listed on CanvasFeature's conf
>> variable list on the wiki.  Fixed that just now). See
>> http://gmod.org/wiki/JBrowse_Configuration_Guide#CanvasFeatures_Configuration_Options
>>
>> maxFeatureScreenDensity is number of features per screen pixel,
>> measured horizontally.  It defaults to 1 in CanvasFeatures tracks, or
>> 1.5 in Alignments2 tracks.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 12/31/2013 11:32 AM, Keiran Raine wrote:
>>> Hi,
>>>
>>> Can I define the point that the switch between the BAM Alignment2 and
>>> the new BW histogram option?  I've got the example
>>> <https://github.com/GMOD/jbrowse/blob/90debb6fc14066b55d7f7464124cd2fe802eeab6/docs/tutorial/data_files/volvox-sorted.bam.conf#L7>
>>> from
>>> the sample dataset but I don't see an option for this.  I want to define
>>> 10,000 bp as the max region for Alignment2 and to be the point that we
>>> switch to histogram.
>>>
>>> Apologies if this has been answered over the last couple of weeks and
>>> I've missed it in the stack of emails.
>>>
>>> Thanks, and happy new year to all,
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> [hidden email] <mailto:[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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affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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