Implement GWAS catalog SNP tick track about igv.js HOT 6 CLOSED

An approximate roadmap.

• decide on a type identifier for the new custom forma. decided. its "gtexGWAS"
• create small example file and put in test / data folder
• extend igv.FeatureParser to handle the new file type by implementing a new decode function. The function should return an object with a minimum of 3 properties: chr, start, end. Look at decodePeak in the file feature/igv.Feature for a model. This function can be passed in to the FeatureParser constructor, but for now just stick it in the file and add a new entry to the switch/case in the constructor.
• write a unit test for the new parser in the test folder. Use testBED.html and testBED.js as a model
• "run" unit test by opening its html in a browser
• you should now be able to create a track using a config option similar to this

{ type : 'gtexGWAS', url 'http://.....', label : 'GWAS track' }

• discuss next step with Jim...

** NOTE: start position of feature should be in zero based coordinates. For a snp subtract 1 from the value in the file for the start position. The end position == value in the file.

from igv.js.

The branch that the changes are on is kane_2April2015_gtexGWAS

from igv.js.

Kane, how does latest grunt "break build"? I don't want to merge the
grunt file "WORKS_LOCAL_BRE..." into master. We need to fix the
standard grunt file before the merge. Open a git issue and describe
the problem.

On 4/14/15 11:35 AM, khadley wrote:

The branch that the changes are on is kane_2April2015_gtexGWAS

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#65 (comment).

from igv.js.

From the git log it looks like Doug added that file and I inherited it when I did a rebase to keep my branch up to date with any changes made in master.

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Ahh, o.k., I'll delete it then. Should have checked the log, sorry.

On Tue, Apr 14, 2015 at 1:14 PM, khadley [email protected] wrote:

From the git log it looks like Doug added that file and I inherited it
when I did a rebase to keep my branch up to date with any changes made in
master.

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#65 (comment)
.

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Support for basic track is done. Still needs work on popup text, will open a new issue

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