This may be a rehash of an earlier issue, but I'm trying to figure out why is it that summarizeOverlaps is giving me no reads in a set of bam files.  In essence, when analyzing a set of bam files I got 0 reads after summarizeOverlaps, even if the bam files (a total of 30 of them) show an average of 25M reads each.  The code in R:

mm10.txdb <- makeTxDbFromUCSC(genome="mm10", tablename="knownGene")

ebg10 = exonsBy(mm10.txdb,by="gene")
bamdir = dir(getwd(),pattern = ".bam",full.names=TRUE)
bfl=BamFileList(bamdir,yieldSize=50000,index=character())

overlaps = summarizeOverlaps(features=ebg10,
                             reads=bfl,
                             mode="Union",
                             ignore.strand=TRUE,
                             singleEnd=TRUE)

rnaseq.counts = assays(overlaps)$counts

The "overlaps" object gives me no read counts at all, and if I do an earlier suggestion from an earlier post in including the inter.feature=FALSE flag I still get no reads.  I'm wondering if you guys have ideas on what else may be going on and/or how to move past this.  Thanks!