[Bioc-sig-seq] IRanges - coverage

[Patrick Aboyoun]

Hans-Ulrich,
Thanks for finding the coverage bug for IRanges objects when the  
coverage is 0 everywhere. I forgot to allocate the necessary length 1  
vectors at the C level to store the rle information. I checked in  
fixes to both the BioC 2.3 and BioC 2.4 code lines.  It will take a  
day or so to come through the build system, but when they are  
available they will be versions 1.0.8 (BioC 2.3) and 1.1.9 (BioC 2.4).  
You could always check out the IRanges package directly from svn and  
build the package yourself if you need it sooner.

Cheers,
Patrick


> library(IRanges)
> myRanges = IRanges(start=c(10,20,30,100), width=5)
> myCov = coverage(myRanges, start=50, end=80)
> myCov
   31-integer "XRleInteger" instance
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> sessionInfo()
R version 2.9.0 Under development (unstable) (2008-12-02 r47033)
i386-apple-darwin9.5.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] IRanges_1.1.9

loaded via a namespace (and not attached):
[1] Matrix_0.999375-16 grid_2.9.0         lattice_0.17-17



Hans-Ulrich Klein wrote:
> Dear List,
>
> I find this behavior of the coverage function quite inconvenient:
>
> > myRanges = IRanges(start=c(10,20,30,100), width=5)
> > myCov = coverage(myRanges, start=50, end=80)
> > myCov
>   31-integer "XRleInteger" instance
>  [1] Error in x at values[group, drop = TRUE] : subscript out of bounds
>
> When I apply the coverage function, I do not care whether there are  
> is at least one sequence within the specified region. I think, it  
> would be more sensible to return an XRleInteger object with 31 "0"  
> in the situation above.
>
> Best wishes,
> Hans-Ulrich
>
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