Score value

[SergejN]

Dear Tophat team,

i recently found a small bug in the generated *.bed files. According to the BED format, the value of score must be in the range [0,1000], while TopHat defines the score as the number of reads that support the feature, e.g. an exon-exon junction. Therefore, sometimes the score exceeds the limits and causes the downstream tools to fail.

I do realize that it can be fixed by a simple one-liner that modifies the files before they are analyzed, but it's a bit inconvenient.

Thanks a lot!
Sergej