[BioC] faster way to get differential calls from pileup?

[Hollis Wright]

Hi, all; I've got a pair of lanes of exome sequencing data; we've  
generated pileup files from samtools and we're interested in looking  
for discordant calls for quality control or snp discovery. As best I  
can figure out the way to do this involves doing a findOverlaps and  
the programatically iterating through the match matrix to get the  
matching positions and check for differences. However, the overlap  
finding takes several hours, and since we anticipate there being many  
lanes in the future I'm curious if there's a faster or better way to  
go about this sort of process. Thanks...

Hollis Wright

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