[Bioc-devel] support for BEDPE import/export in rtracklayer?

[Aaron Lun]

Hi all,

Are there any plans to add import/export support for the BEDPE format in
rtracklayer?

http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format

I'd imagine that a hypothetical import method would return a GRangesList
of length equal to the number of rows, where each internal GRanges has
two entries representing the paired regions for the corresponding row.
Extra interaction-specific metadata fields (e.g., score, user-defined
fields) could be stuffed into the GRangesList's elementMetadata slot.
The same object would also be used for export to the BEDPE format.

This functionality would be useful for people working on structural
variations, genomic interactions, etc. for which BEDPE is often used.
The GenomicInteractions package has already got something for this, but
it seems like rtracklayer would be a better (i.e., more general) home
for that kind of function. If anyone's interested, we (i.e., Malcolm and
Liz, the GenomicInteractions developers) would be willing to help
migrate it over.

Cheers,

Aaron (+ Malcolm and Liz)