[BioC] summarizeOverlaps mode ignoring inter feature overlaps

[Thomas Girke]

Dear Valerie,

Is there currently any way to run summarizeOverlaps in a feature-overlap
unaware mode, e.g with an ignorefeatureOL=FALSE/TRUE setting? Currently,
one can switch back to countOverlaps when feature overlap unawareness is
the more appropriate counting mode for a biological question, but then
double counting of reads mapping to multiple-range features is not
accounted for. It would be really nice to have such a feature-overlap
unaware option directly in summarizeOverlaps. 

Another question relates to the memory usage of summarizeOverlaps. Has
this been optimized yet? On a typical bam file with ~50-100 million
reads the memory usage of summarizeOverlaps is often around 10-20GB. To
use the function on a desktop computer or in large-scale RNA-Seq
projects on a commodity compute cluster, it would be desirable if every
counting instance would consume not more than 5GB of RAM.

Thanks in advance for your help and suggestions,

Thomas