NSBS object error when trying to filter by overlap GRanges object from read_bam()

[mce13]

Hi there,

I seem to be unable to perform filtering by overlap on a GRanges object that has been imported from a bam-file via read_bam().

I can run the example code here with no problems.

With my own bam-file, however, and also a miniature version thereof, I get the following error:

roi <- 	data.frame(seqnames = "chrI", start = 4200, end = 4800) %>%
		as_granges()

rng <- 	read_bam(file = "test.bam",
		index =	"test.bam.bai",
		paired  =	TRUE) %>%
	select(mapq) %>%
	filter_by_overlaps(roi)
		
print(rng)

Error: subscript is a NSBS object that is incompatible with the current
  subsetting operation
Execution halted

The join_overlap functions give me the same error.

The bam-file is paired end. It has been generated by mapping public data (SRX372005) against SacCer3 using bowtie2 with the default settings. test.bam was generated using samools view and indexed using samtools index. I'm happy to upload/email these files but it seems that bam-files are not supported.

Any idea what the problem could be here?

Many thanks in advance,

mce13