Changing default colors for LOH track

[Shireen]

I am using .seg file with LOH info, and I cannot change the color of the LOH:

here is my file, and first couple rows

#type=LOH
#track maxHeightPixels=30:60:90 color=255,255,224  altColor=128,0,128
sample ID chromosome start stop loh (0 or 1)
0007153_A01.OSCHP 1 754192 3635788 0
0007153_A01.OSCHP 1 3639884 16302982 1
0007153_A01.OSCHP 1 16321010 17681277 0

IGV does change the track height, but not the color. 

thanks!

Shireen

[James Robinson]

Could you attach this segment as a file?  The problem could be improper whitespace (e..g tabs instead of spaces in the track line),  and whitespace is not preserved when you copy/paste to the forum.

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[Shireen]

thanks--I have attached it as a file.

Shireen

[James Robinson]

Hi,

The problem was a color scale exists for "type=loh",  so your values were ignored.   The trick is to set type to "other".   There were a couple of other problems with your example file, it was missing "#track"  and there was an extra space in the track line.  Try the attached

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