On Mon, Nov 12, 2012 at 10:54 AM, Cook, Malcolm <MEC@stowers.org> wrote:

> > The end = start - 1 encoding for zero-width Ranges objects has existed as
> > long as the IRanges package. Having end < start is obviously not ideal,
> but
> > there are no clearly superior alternatives.
>
> Hi,
>
> Was it ever considered allowing two out of three start end width equal to
> NA, to mean 'unknown' or 'unspecified'?
>
> We could have IRanges of a known width, but an unknown start or stop.
>
> Or a GRanges of a known chomosome and start and strand, but unknown stop
> or width.
>
> Or a known width but unknown start or stop.
>
> I'm sure allowing such would wreck havoc in a million other places.
>
> Just wondering if the conversation was had and how it went....
>
>
It was discussed, it was probably punted until there was a clear use case.
This is a different issue from zero-width ranges, of course.

Michael



> ;)
>
> ~Malcolm
>
>
> >
> > Michael
> >
> > On Mon, Nov 12, 2012 at 8:58 AM, Kasper Daniel Hansen <
> > kasperdanielhansen@gmail.com> wrote:
> >
> > > Well, I am surprised by the zero width IRanges with start and end.
> > > The choice of start = 5 and end = 4 is - as far as I can see -
> > > completely arbitrary.  I also don't like the fact that start() and
> > > end() just reports 5 and 4 - I could see myself making mistakes in my
> > > code, because I believe I assume start <= end.
> > >
> > > But perhaps this is because it is now allowed to have zero-width
> IRanges?
> > >
> > > Kasper
> > >
> > >
> > > On Mon, Nov 12, 2012 at 6:20 AM, Vincent Carey
> > > <stvjc@channing.harvard.edu> wrote:
> > > > does this contradict the doc in some way?  the second range of your
> > > result
> > > > has width zero, which i think is correct.
> > > >
> > > > On Sun, Nov 11, 2012 at 12:16 PM, Kasper Daniel Hansen
> > > > <kasperdanielhansen@gmail.com> wrote:
> > > >>
> > > >> Example
> > > >>
> > > >> library(GenomicRanges)
> > > >> gr1 = GRanges(seqnames = c("chr1", "chr1"), ranges = IRanges(start =
> > > >> c(1,5), width = 7))
> > > >> gr2 = GRanges(seqnames = "chr1", ranges = IRanges(start = 1, end =
> 4))
> > > >> pintersect(gr1, rep(gr2, 2))
> > > >>
> > > >> GRanges with 2 ranges and 0 metadata columns:
> > > >>       seqnames    ranges strand
> > > >>          <Rle> <IRanges>  <Rle>
> > > >>   [1]     chr1    [1, 4]      *
> > > >>   [2]     chr1    [5, 4]      *
> > > >>   ---
> > > >>   seqlengths:
> > > >>    chr1
> > > >>      NA
> > > >>
> > > >> The second element in the return GRanges should be empty.  I would
> > > >> therefore expect that the return length of the pintersect would have
> > > >> length 1, despite the fact that the first object has length 2.
> > > >>
> > > >> Kasper
> > > >>
> > > >> _______________________________________________
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> > > >
> > > >
> > >
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