Hi,
I got two more (with VariantAnnotation_1.9.35, Rsamtools_1.15.27). They
may be related to what we discussed before, so I'm leaving them in this
thread.
** Some example data
#+BEGIN_SRC R
library(VariantAnnotation)
example(VRanges) ## gives us 'vr' and 'vcf'
vr_small = vr
On Fri, Feb 7, 2014 at 12:09 AM, Julian Gehring julian.gehr...@embl.dewrote:
Hi,
I got two more (with VariantAnnotation_1.9.35, Rsamtools_1.15.27). They
may be related to what we discussed before, so I'm leaving them in this
thread.
** Some example data
#+BEGIN_SRC R
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
Hi Julian,
Thanks for this one. It was a bug in Rsamtools, now fixed in devel, version
1.15.27. I'll leave it to Martin/Val to OK it and push to release.
Michael
On Thu, Feb 6, 2014 at 1:46 AM, Julian Gehring julian.gehr...@embl.dewrote:
Hi Michael,
Thanks for the fast patching. However,
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,
Thanks, fixed in 1.9.35/1.8.11.
On Wed, Feb 5, 2014 at 12:35 AM, Julian Gehring julian.gehr...@embl.dewrote:
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
