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VCF - field formatting patterns #421

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keiranmraine opened this Issue Jan 20, 2014 · 1 comment

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@keiranmraine
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keiranmraine commented Jan 20, 2014

The default VCF popup for variants is generally fit for most uses. In some cases however I just want to be able to split an entry so that it spans multiple lines, e.g.

screen shot 2014-01-20 at 13 45 06

Is it possible to have some sort of minimal callback to change behaviour for a single field rather than re-implement the whole popup content? For example

VCF.info.VD=split /\|/

would be sufficient in this case (perl for illustration purposes only).

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cmdcolin Mar 3, 2014

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Hi Kieran,
I just added some basic support to do the this type of customization of the detail popups.

Here is an example config for a vcf file

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = MyVariants.vcf.gz

# settings for how the track looks
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = My Variants

# new customization callbacks
fmtDetailValue_VD = function(value) { return value.split('|'); }
fmtDetailField_VD = function(title) { return "Variant description"; }

Great idea btw. I think someone could easily add things like external links with this feature too. This feature should be out in the next release and if you have any problems let me know!

Contributor

cmdcolin commented Mar 3, 2014

Hi Kieran,
I just added some basic support to do the this type of customization of the detail popups.

Here is an example config for a vcf file

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/VCFTabix
urlTemplate    = MyVariants.vcf.gz

# settings for how the track looks
category = VCF
type = JBrowse/View/Track/CanvasVariants
key  = My Variants

# new customization callbacks
fmtDetailValue_VD = function(value) { return value.split('|'); }
fmtDetailField_VD = function(title) { return "Variant description"; }

Great idea btw. I think someone could easily add things like external links with this feature too. This feature should be out in the next release and if you have any problems let me know!

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