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Introduction

For many text-based file formats, it is possible to configure the track name, color, and display properties through the use of track lines in the file header or comments.

Track lines were invented for use in the UCSC genome browser, and the full format is described on the UCSC Genome Bioinformatics web site.

IGB understands a subset of the full format, and will ignore property settings that it doesn't use.

Track line syntax

In ".wig", ".bed", ".psl", or "gff" format (version 1 or 2), the track line begins with "track".

In ".gff" format version 3, the track line must begin with "##track" to indicate it as a meta-directive, since track lines would otherwise disobey the GFF3 specification.

GFF3 has its own rich methods of specifying annotation styles. A future version of IGB may make use of this.

Here is a sample track line that can be understood by IGB:

track name="Example" description="Example Description" visibility=full color=200,100,0 useScore=1 url="http://sample.com/search?id=$$"

Supported track line properties

IGB understands these track line properties:

name

Short track name.

color

Track color, in the format r,g,b; where r, g, and b are numbers from 0 to 255.

description

Human-readable short description of the track.

visibility

In IGB, visibility=1 and visiblity=dense will cause the track to be displayed in "collapsed" mode. Otherwise, the track displays in "expanded" mode.

url

A URL for linking to an outside website.  Any instances of $$  in the URL will be replaced with the item id.  See  Configuring Web links (LinkOuts) to external sites.

useScore

Whether to convert score data to color values.  Valid values are useScore=0 and useScore=1 Files in ".bed" and ".gff" format can contain scores.  

itemRgb

If itemRgb=On, use the data in column 9 of ".bed" files to determine the colors of individual annotations.  Using this function requires additional memory.

graphType

Sets the graph type for graph files in the "wiggle" format.  Can be graphType=bar or graphType=points.  

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