[Bioc-devel] as.list of a GRanges

[Michael Lawrence]

On Thu, Feb 15, 2018 at 11:53 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
>
> Can I ask, is this change under discussion in current release or so far in
> Bioconductor devel only (my assumption)?
>
>  > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
>  > > So is as.list() no longer supported for GRanges objects? I have found
> it
>  > > useful in places.
>  >
>  > Very few places. I found a dozen of them in the entire software repo.
>
> However there are probably more in the wild...
>
>
Yes, this is what I meant. The Bioc package corpus is not very
representative for some of these entry points. Please keep that in mind
when making refactoring decisions.


>  > Now you should use as.list(as(gr, "GRangesList")) instead.
>  > as.list() was behaving inconsistently on IRanges and GRanges objects,
>  > which is blocking new developments. It will come back with a consistent
>  > behavior. More generally speaking IRanges and GRanges will behave
>  > consistently as far as their "list interpretation" is concerned.
>
>
Please be careful with these changes in behavior. Given the amount of code
that now depends on this software, consistency with existing behavior needs
to be weighted heavily.


> Can we please be assured to be reminded of this prominently in release
> notes?
>
> Thanks!
>
> ~malcolm
>

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