Message-ID: <4EEAA4CC.1070106@fhcrc.org>
Date: 2011-12-16T01:54:20Z
From: Martin Morgan
Subject: [Bioc-devel] Rsamtools scanTabix Method Dispatch
In-Reply-To: <20111216110011.BPH28508@gimr.garvan.unsw.edu.au>
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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