[BioC] bug in pintersect in GenomicRanges

[Kasper Daniel Hansen]

Hmm, ok.

Well, an alternative is to let the output of pintersect be shorter
than the two inputs.  Also, compare to
  intersect(gr1[2], gr2)
which is empty.

Kasper



On Mon, Nov 12, 2012 at 1:46 PM, Michael Lawrence
<lawrence.michael at gene.com> 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.
>
> 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
>> >>
>> >> _______________________________________________
>> >> Bioconductor mailing list
>> >> Bioconductor at r-project.org
>> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>