BED parsing and rendering

[sourabh2k15]

Please review and let me know if any changes are required.
preview : http://i.imgur.com/B0RhJTr.png

[simonbrent]

feature.chromStart has not been set - did you mean feature.start?
Also, feature.drawThickBlock is never used anywhere.

[simonbrent]

Please remove console.logs

[simonbrent]

Please remove console.logs

[simonbrent]

Please give a radix argument (10) for parseInt

[simonbrent]

Only assign feature.subFeatures if subfeatures.length is not 0

[simonbrent]

You shouldn't need to define a view here - you can leave the properties below on the track prototype (as the were previously). Also, populateMenu is a Controller function, not a View function, so it [probably] won't work at the moment

[simonbrent]

Why do you pop these arrays?

[sourabh2k15]

because the blockSizes and blockStarts fields are of the form 1,2,3,4,
the ending comma leads to an extra empty element when we split the above string using ',' as delimiter.

[simonbrent]

Hmm, the example here https://genome.ucsc.edu/FAQ/FAQformat#format1 is

track name=pairedReads description="Clone Paired Reads" useScore=1
chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512
chr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601

which has a trailing comma on blockSize but not on blockStart. I think it would be better to have them both defined as

fields[10 or 11].split(",").filter(function (n) { return n; })

That way we can be sure of not losing the last value if it exists

[sourabh2k15]

I have implemented changes as per your comments. Also please help me figure out how to use thickStart and thickEnd. I did not get any hints from ucsc as to how they are rendered, so I haven't used them at the moment .

[simonbrent]

re thickStart/thickEnd: what I understand from the description ("The starting position at which the feature is drawn thickly") is that between start and thickStart, and thickEnd and end, the subFeatures are drawn at one height, but between thickStart and thickEnd they are drawn with a greater height.

This reflects how transcripts are currently drawn, to a certain extent.

You can implement this by giving a thickHeight property to Track.File.BED, and then in Model.File.BED.parseData, set subfeature.height = this.prop('thickHeight') if subfeature.start and subfeature.end are between thickStart and thickEnd.

It may also be necessary to split a subfeature into two (one with height = thickHeight, the other without), if the subfeature is only partially within the thickStart-thickEnd region.

If there is a thickHeight region of the feature, the feature's height will need to be set to thickHeight too, in order to ensure correct positioning and drawing.

Incidentally, you're currently setting subfeature.height = 7 for each subfeature. It would be better to remove this line and set Track.File.BED.featureHeight = 7 instead of 6, if you think 6 is too small (7 and 10 are the heights used in Track.View.Transcript, so I think this is fine).

[sourabh2k15]

Hello simon, I have added the change as you have said and removed pop() in favor of filter() to not lose last elements.