[Gmod-ajax] chunkSizeLimit not being honoured for local files

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[Gmod-ajax] chunkSizeLimit not being honoured for local files

Keiran Raine
Hi,

We’re having problems with some very deep sequenced but sparse files (amplicon sequencing).  As we know these are very deep we want to raise the max data value from 5MB.

This should be possible via ‘chunkSizeLimit’ and I know it works if done for configurations loaded from the server but it appears that modifying a track directly (edit config) has no effect.  The usual section warning appears indicating that the segment is >5MB (5,000,000), even when set to 150,000,000 as below:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 6000000,
  "glyph": "JBrowse/View/FeatureGlyph/Alignment",
  "maxFeatureGlyphExpansion": 0,
  "maxHeight": 600,
  ...
  "displayMode": "normal",
  ...
  "chunkSizeLimit": 150000000,
  "label": "BAM_179094_1",
  "key": "BAM 179094",
  "type": "JBrowse/View/Track/Alignments2",
  "category": "Local tracks",
}

Is this actually broken?  I’ve tried setting this using ‘edit config’ during the track load stage too, it ends up in the track config available after loading but the behaviour remains unchanged.

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 not being honoured for local files

Colin
Hi Keiran

I might agree that this is a bug. I think generally, the "chunkSizeLimit" is passed into an argument for the "BAM store" class, but the issue is that the store does not get reinitialized when you use the "Edit config" (AFAIK), so I think that is why the "Edit config" to increase the limit doesn't fix the issue. 

Not sure if there are any workarounds, I would say generally it would be best if some code could handle the sparse BAM file stats estimation better (ref https://github.com/GMOD/jbrowse/issues/540).

-Colin

On Fri, Mar 18, 2016 at 6:54 AM, Keiran Raine <[hidden email]> wrote:
Hi,

We’re having problems with some very deep sequenced but sparse files (amplicon sequencing).  As we know these are very deep we want to raise the max data value from 5MB.

This should be possible via ‘chunkSizeLimit’ and I know it works if done for configurations loaded from the server but it appears that modifying a track directly (edit config) has no effect.  The usual section warning appears indicating that the segment is >5MB (5,000,000), even when set to 150,000,000 as below:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 6000000,
  "glyph": "JBrowse/View/FeatureGlyph/Alignment",
  "maxFeatureGlyphExpansion": 0,
  "maxHeight": 600,
  ...
  "displayMode": "normal",
  ...
  "chunkSizeLimit": 150000000,
  "label": "BAM_179094_1",
  "key": "BAM 179094",
  "type": "JBrowse/View/Track/Alignments2",
  "category": "Local tracks",
}

Is this actually broken?  I’ve tried setting this using ‘edit config’ during the track load stage too, it ends up in the track config available after loading but the behaviour remains unchanged.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank">+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 not being honoured for local files

Keiran Raine
Hi Colin,

FYI, this also doesn’t take effect even when you edit the config in advance on file open dialogues:



Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 27 Mar 2016, at 18:07, Colin <[hidden email]> wrote:

Hi Keiran

I might agree that this is a bug. I think generally, the "chunkSizeLimit" is passed into an argument for the "BAM store" class, but the issue is that the store does not get reinitialized when you use the "Edit config" (AFAIK), so I think that is why the "Edit config" to increase the limit doesn't fix the issue. 

Not sure if there are any workarounds, I would say generally it would be best if some code could handle the sparse BAM file stats estimation better (ref https://github.com/GMOD/jbrowse/issues/540).

-Colin

On Fri, Mar 18, 2016 at 6:54 AM, Keiran Raine <[hidden email]> wrote:
Hi,

We’re having problems with some very deep sequenced but sparse files (amplicon sequencing).  As we know these are very deep we want to raise the max data value from 5MB.

This should be possible via ‘chunkSizeLimit’ and I know it works if done for configurations loaded from the server but it appears that modifying a track directly (edit config) has no effect.  The usual section warning appears indicating that the segment is >5MB (5,000,000), even when set to 150,000,000 as below:

{
  "maxFeatureSizeForUnderlyingRefSeq": 250000,
  "maxFeatureScreenDensity": 6000000,
  "glyph": "JBrowse/View/FeatureGlyph/Alignment",
  "maxFeatureGlyphExpansion": 0,
  "maxHeight": 600,
  ...
  "displayMode": "normal",
  ...
  "chunkSizeLimit": 150000000,
  "label": "BAM_179094_1",
  "key": "BAM 179094",
  "type": "JBrowse/View/Track/Alignments2",
  "category": "Local tracks",
}

Is this actually broken?  I’ve tried setting this using ‘edit config’ during the track load stage too, it ends up in the track config available after loading but the behaviour remains unchanged.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:<a href="tel:%2B44%20%280%291223%20834244%20Ext%3A%207703" value="+441223834244" target="_blank" class="">+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.

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
_______________________________________________
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.

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
_______________________________________________
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