[BioC] read counts in sliding windows

[Jason Lu]

Hi list,

I would like to seek your advice with this.
Here I have a GRangesList and a GappedAlignments objects (an alignment
to the genome). For each GRanges (with length 1) in the GRangesList, I
would like to do a sliding window on its ranges and count reads from
each window. So far I wasn't able to find an efficient way to do this.
My problem is similar to this one:
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/34431.
But looping over the GRangesList (and using countOverlaps inside the
loop) takes significant time.

Thanks for any suggestions.

Best,

Jason