url chromStart $[ position incorrect

[Denise Mauldin]

Hi all,

I'm attempting to create a custom track for Kaviar.  My track line is:

track name=Kaviar description="Kaviar Allele Frequencies" visibility=squish useScore=1 url="http://db.systemsbiology.net/kaviar/cgi-pub/Kaviar.pl?db=hg19&chr=$S&&pos=$["

Example line:

chr2 279694 279695 "Kaviar_MAF:C=0.0003791" 949

This loads properly:

Kaviar Allele Frequencies

Outside Link:
Item: "Kaviar_MAF:C=0.0003791"
Score: 949
Position: chr2:279695-279695
Band: 2p25.3
Genomic Size: 1

However, when I click on Outside link, it seems to think that $[ is the position of the window of the view that was in the browser when I clicked on the track information.  I thought that $[ would be the start position of the feature (aka 279695).  What is the variable for the start position of the feature to include in the url track info?  Do I instead need to include the start position in the name something like 'Kaviar_MAF:279695:C=0.0003791'?

Thanks,

Denise

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Denise Mauldin | Senior Software Engineer

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[Christopher Lee]

Hi Denise,

Thank you for reporting this. The $[ and $] are intended to refer to the start and end
position of the current window, we were not clear enough with our documentation regarding
this. We will be fixing the documentation in addition to adding two new variables to support
item start and end positions. These will be released in an upcoming version, after they have
passed testing by our Quality Assurance team.

I have made a note to contact you once the feature is released.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Christopher Lee]

Hi Denise,

We have added two new variables, ${ and $}, to indicate item boundaries. $[ and $] still refer to the window boundaries as they did before.

For more information please see the following page:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#url

Please let us know if you are having further problems!

Thanks,

Christopher Lee
UCSC Genomics Institute

On Thu, Jul 28, 2016 at 12:45 PM, Christopher Lee <chm...@ucsc.edu> wrote:

Hi Denise,

Thank you for reporting this. The $[ and $] are intended to refer to the start and end
position of the current window, we were not clear enough with our documentation regarding
this. We will be fixing the documentation in addition to adding two new variables to support
item start and end positions. These will be released in an upcoming version, after they have
passed testing by our Quality Assurance team.

I have made a note to contact you once the feature is released.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

[Denise Mauldin]

Hi Christopher,

Thank you very much!

Best,

Denise