[Bioc-devel] Rsamtools Reading TabixFile URL

Dario Strbenac D.Strbenac at garvan.org.au
Fri Dec 23 00:00:10 CET 2011


yieldTabix won't work when the file is a URL. Here is an example.

txTabix <- open(TabixFile("http://savantbrowser.com/data/hg18/hg18.refGene.gz"))

Also, I thought yieldSize was a maximum, not that it had to be that big :

> txTabix <- TabixFile(system.file("extdata", "example.gtf.gz", package="Rsamtools"))
> txGR <- yieldTabix(txTabix, yieldSize = Inf)
Error: yield: negative length vectors are not allowed
> txGR <- yieldTabix(txTabix, yieldSize = .Machine$integer.max)
Error: yield: cannot allocate vector of size 16.0 Gb

What is the most efficient way to read in all records, without over-allocating RAM ?

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

More information about the Bioc-devel mailing list