It's a shame that the format violates the BEDX+Y convention by inserting the second chr, start and end before some of the canonical BED fields.
Anyway, I think it would be great if you guys could contribute a parser. Maybe just fork the github mirror? Michael On Tue, Dec 8, 2015 at 1:24 PM, Aaron Lun <[email protected]> wrote: > 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) > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
