[Bioc-devel] Rsamtools scanTabix Method Dispatch

[Martin Morgan]

On 12/15/2011 04:00 PM, Dario Strbenac wrote:
> Hello,
>
> This looks like a bug.
>
> library(Rsamtools)
>
> gr<- GRanges("chr1", IRanges(1, 999999999))
> txs<- scanTabix("http://savantbrowser.com/data/hg18/hg18.refGene.gz", param = gr)
>
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function "scanTabix", for signature "TabixFile", "missing"
>
> I have Rsamtools_1.6.2 in R version 2.14.0 (2011-10-31)
>
> One more related question. Is it possible to get all records from a tabix file without looping over each chromosome and collapsing the list at the end ?
>

Hi Dario --

Thanks for the bug report; look for version 1.6.3 for a fix.

Use yieldTabix to get consecutive chunks of the file (including the 
whole thing in one big chunk).

example(yieldTabix)
res <- yieldTabix(TabixFile(fl))

Martin

> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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