Entering edit mode
Richard Pearson
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80
@richard-pearson-5255
Last seen 9.6 years ago
Hi
I've noticed a bug with writeVcf when trying to write out relatively
simple vcf files, e.g. a file containing only GT in the FORMAT fields.
The following is a (hopefully) reproducible example based on examples
in
?writeVcf
library(VariantAnnotation)
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
out1.vcf <- tempfile()
out2.vcf <- tempfile()
in1 <- readVcf(fl, "hg19")
writeVcf(in1, out1.vcf)
in2 <- readVcf(fl, "hg19", ScanVcfParam(geno="GT"))
writeVcf(in2, out2.vcf)
This last line gives me:
Error in row(genoMat) :
a matrix-like object is required as argument to 'row'
Looking at the following code snippet from .makeVcfGeno, it seems
genoMat is first getting created as a matrix, but then changed to
something that is not a matrix by "genoMat <- genoMatFlat". The error
then comes from the "row(genoMat)" on the last line shown. I don't
really understand what is going on in this code so can't offer a patch
I'm afraid.
genoMat <- matrix(unlist(as.list(geno), use.names = FALSE,
recursive = FALSE), nsub * nrec, length(geno))
genoMatFlat <- as.character(unlist(genoMat))
genoMatFlat[is.na(genoMatFlat)] <- "."
if (is.list(genoMat)) {
genoMatList <- relist(genoMatFlat,
PartitioningByEnd(genoMat))
genoMatFlat <- .pasteCollapse(genoMatList, ",")
genoMat <- matrix(genoMatFlat, nrow(genoMat), ncol(genoMat))
}
else genoMat <- genoMatFlat
formatMatPerSub <- matrix(rep(t(formatMat), nsub), nsub *
nrec, length(geno), byrow = TRUE)
keep <- !is.na(formatMatPerSub)
genoListBySub <- seqsplit(genoMat[keep], row(genoMat)[keep])
FWIW, as a temporary fix I made an extra, slightly more complex FORMAT
field using the following:
geno(in2)[["DUMMY"]] <- matrix(sapply(as.vector(geno(in2)[["GT"]]),
function(x) list(c(x, x))), ncol=ncol(geno(in2)[["GT"]]),
dimnames=dimnames(geno(in2)[["GT"]]))
writeVcf(in2, out2.vcf)
I've checked and it seems this bug is also present in latest devel.
Any
chance of a fix?
Thanks
Richard
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8
LC_MESSAGES=en_GB.UTF-8 LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.4.5 Rsamtools_1.10.2 Biostrings_2.26.2
GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0
devtools_0.8 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0
bitops_1.0-5 BSgenome_1.26.1 DBI_0.2-5 digest_0.6.0
evaluate_0.4.2 GenomicFeatures_1.10.1 httr_0.2
[11] memoise_0.1 parallel_2.15.1 plyr_1.7.1
RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.18.1
stats4_2.15.1 stringr_0.6.1 tools_2.15.1
whisker_0.1
[21] XML_3.95-0.1 zlibbioc_1.4.0
