[BioC] Wig files?

[Ed Siefker]

What do I use to handle .wig files in a fast and convenient manner?

I have a bunch of .wig files from the TCGA.  All I want to know is
if a single position was sufficiently covered by the sequencer to
call a mutation.  This is represented by a '1' at the appropriate
line in the file.   Insufficient coverage is represented by a '0'
or the lack of any lines corresponding to those coordinates.

'rtracklayer' seems to be the package people use to handle
.wig files.   So I started R, installed 'rtracklayer' and executed:
wigtest  <- import("TCGA-A6-3807.wig", asRangedData = FALSE)
as indicated in the documentation.

So far, it's been about 3 hours of maxed out CPU.  What is
'rtracklayer' doing?  Sure, it's a 91mb .wig, but I can grep
the thing in less than 1s. Is this expected behavior?  Should
I be going about this in a different way?