[BioC] bug in pintersect in GenomicRanges

[Cook, Malcolm]

> 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....

;)

~Malcolm


> 
> Michael
> 
> On Mon, Nov 12, 2012 at 8:58 AM, Kasper Daniel Hansen <
> kasperdanielhansen at 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 at 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 at 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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