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

[Michael Lawrence]

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 <alun at wehi.edu.au> 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)
>
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