[BioC] Using summarizeOverlaps with multiple samples/readgroups in a single bam file?

[Ryan C. Thompson]

Hi all,

I'm looking at simplifying my differential expression pipeline a little 
bit by merging all my input bam files into one bam file with multiple 
samples/read groups and then using that bam file as input to 
summarizeOverlaps. Is this supported in any way? I've never worked with 
sam read groups before (I always just did one sample per file), so I 
don't really know anything about them.

So is it supported to take a single bam file and use summarizeOverlaps 
or some other mechanism to get a SummarizedExperiment object with one 
column for each sample in the bam file, rather than one column per file?

-Ryan Thompson