[Bioc-devel] VariantAnnotation: writeVcf fails for factors with unused levels
Hi Michael,
Thanks for the fast patching. However, going a step further and trying
to read the VCF again fails (with VariantAnnotation_1.9.35
). I'm not sure if this is related to the same issue.
#+BEGIN_SRC R
library(VariantAnnotation)
example(VRanges)
writeVcf(vr, "out.vcf") ## works
readVcf("out.vcf", "hg19") ## fails
#+END_SRC
Error in `rownames<-`(`*tmp*`, value = c("chr1", "chr2")) :
invalid rownames length
Best wishes
Julian
On 02/05/2014 08:38 PM, Michael Lawrence wrote:
Thanks, fixed in 1.9.35/1.8.11. On Wed, Feb 5, 2014 at 12:35 AM, Julian Gehring <julian.gehring at embl.de>wrote:
Hi,
I just stumbled over the fact that 'writeVcf' for a 'VRanges' fails if
'sampleNames' is a factor with unused levels. Here a small example:
#+BEGIN_SRC R
library(VariantAnnotation)
example(VRanges)
writeVcf(vr, "out.vcf") ## works
f = sampleNames(vr)
f ## levels: a, b
levels(f) = c("a", "b", "c") ## c in unused
f ## levels: a, b, c
sampleNames(vr) = f
writeVcf(vr, "out.vcf") ## fails
#+END_SRC
Error in writeVcf(as(obj, "VCF"), filename, ...) :
error in evaluating the argument 'obj' in selecting a method for
function 'writeVcf': Error in ans[sampleToUniq] <- as.vector(v) :
replacement has length zero
This occurs both with the latest bioc-release and bioc-devel. I don't
know what exactly is causing this, but please let me know if I can be of
any help.
Best wishes
Julian
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