Hi,
I'm not sure whether this is related to the other bug. Anyway,
'writeVcf' fails if the sample names of a 'VRanges' object are not
sorted in ascending order (in the latest bioc-devel):
#+BEGIN_SRC R
library(VariantAnnotation)
vr = VRanges(1:2, IRanges(100:101, 200:201),
ref = c("G", "G"), alt = c("A", "T"))
sampleNames(vr) = factor(c("1", "2"))
writeVcf(vr, tempfile()) ## works, also for "A"/"B", etc
sampleNames(vr) = factor(c("2", "1"))
writeVcf(vr, tempfile()) ## fails, also for "B"/"A", etc.
## convertion to VCF itself works
vcf = as(vr, "VCF")
writeVcf(vcf, tempfile()) ## fails
#+END_SRC
with the error:
Error in relist(genoMatFlat, PartitioningByEnd(genoMat)) :
shape of 'skeleton' is not compatible with 'NROW(flesh)'
In bioc-release (VariantAnnotation_1.8.10), it fails irrespective of the
sample name order:
#+BEGIN_SRC R
library(VariantAnnotation)
vr = VRanges(1:2, IRanges(100:101, 200:201),
ref = c("G", "G"), alt = c("A", "T"))
sampleNames(vr) = factor(c("1", "2"))
writeVcf(vr, tempfile()) ## fails
#+END_SRC
with
Error in writeVcf(as(obj, "VCF"), filename, ...) :
error in evaluating the argument 'obj' in selecting a method for
function 'writeVcf': Error in listClassName("Compressed", class(x)) :
Could not find a 'CompressedList' subclass for values of type
'CompressedRleListRleListCompressedAtomicListAtomicListCompressedListListVectorAnnotated'
Please let me know if I can help.
Best wishes
Julian
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