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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=$$"
Supported track line properties
IGB understands these track line properties:
Short track name.
Track color, in the format r,g,b; where r, g, and b are numbers from 0 to 255.
Human-readable short description of the track.
In IGB, visibility=1 and visiblity=dense will cause the track to be displayed in "collapsed" mode. Otherwise, the track displays in "expanded" mode.
A URL for linking to an outside website. Any instances of $$ in the URL will be replaced with the item id. See Configuring Web links (LinkOuts) to external sites.
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.
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.
Sets the graph type for graph files in the "wiggle" format. Can be graphType=bar or graphType=points.