Segway produces annotations that are not stictly valid BED files

[EricR86]

Currently Segway produces annotations with a track header line.

From UCSC BED FAQ

Please note that only in custom tracks can the first lines of the file consist of header lines, which begin with the word "browser" or "track" to assist the browser in the display and interpretation of the lines of BED data following the headers. Such annotation track header lines are not permissible in downstream utilities such as bedToBigBed, which convert lines of BED text to indexed binary files. 

Some tools downstream will simply not work with existing Segway annotations. It might be best considering removing the track header line altogether.

[michaelmhoffman]

We would have done this already except that it will probably break anything that depends on Segway output looking like this, so I think it needs to be a major release change.