I'm using the method on the following URL to convert bed to wig. But
the problem is that if blockCount is greater than 1, the breaks in
between blocks is also counted by bedItemOverlapCount. Is there a
different program to avoid the breaks?

https://lists.soe.ucsc.edu/pipermail/genome/2008-September/017062.html

-- 
Regards,
Peng
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