I have a BED file from an external data source that is tab-separated with spaces in the name field for some rows. These fields are not quoted. Looking at the code for rtracklayer::import.bed, it seems to use read.table with the default separator argument and no option to change it, which means all whitespace is treated as field separators. This causes the import to fail. Would it be possible to add an option to specify the separator when importing BED files?

I just pushed a change to devel that expects all BED files to be tab-separated. That's what the spec says, and it's what bedtools requires, so hopefully it does not cause too much havoc.