[BioC] Bug in subsetting vcf file by subject on more than 5 samples

[Valerie Obenchain]

Now fixed in 1.9.26.

I was using vcfSamples() on a ScanVcfParam to pass the sample names down 
to scanVccf(). This extractor has a fancy show method that for n > 5 
displays a few names and '...' to indicate more. This character '...' 
was being passed as a sample name and triggered the check for 
non-existent sample names.

Thanks for catching this and for providing a reproducible example.

Valerie


On 12/17/2013 03:28 AM, Robert Castelo wrote:
> hi,
>
> when using the recently added feature of subsetting a vcf file by
> subject, described initially here:
>
> https://stat.ethz.ch/pipermail/bioconductor/2013-April/052146.html
>
> i found out that it breaks when the samples to subset are more than 5.
> here is the code reproducing the problem:
>
> suppressPackageStartupMessages(library(VariantAnnotation))
> fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
> hdr <- scanVcfHeader(fl)
> length(samples(hdr))
> [1] 85
>
> so the above example file has 85 samples, let's try to subset on the
> first 6 ones:
>
> param <- ScanVcfParam(samples=samples(hdr)[1:6])
> vcf <- readVcf(fl, "hg19", param)
> Warning message:
> In .vcf_map_samples(samples(hdr), samples) : samples not in file: ‘...’
>
> next to this warning, the resulting 'CollapsedVCF' object has only 4
> samples instead of 6:
>
> dim(vcf)
> [1] 9 4
>
> a hint about what might be happening comes from the sample names in the
> parameter object and the '...' referred to in the warning:
>
> vcfSamples(param)
> [1] "NA06984" "NA06986" "..."     "NA07000" "NA07037"
>
> this happens in both the release and devel versions, here's my
> sessionInfo() for the release version:
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C LC_TIME=en_US.UTF8
>   [4] LC_COLLATE=en_US.UTF8     LC_MONETARY=en_US.UTF8
> LC_MESSAGES=en_US.UTF8
>   [7] LC_PAPER=en_US.UTF8       LC_NAME=C                 LC_ADDRESS=C
> [10] LC_TELEPHONE=C            LC_MEASUREMENT=en_US.UTF8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>    base
>
> other attached packages:
>   [1] VariantAnnotation_1.8.8 Rsamtools_1.14.2        Biostrings_2.30.1
>   [4] GenomicRanges_1.14.4    XVector_0.2.0           IRanges_1.20.6
>   [7] BiocGenerics_0.8.0      vimcom_0.9-92           setwidth_1.0-3
> [10] colorout_1.0-1
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.24.0   Biobase_2.22.0         biomaRt_2.18.0
> bitops_1.0-6
>   [5] BSgenome_1.30.0        DBI_0.2-7 GenomicFeatures_1.14.2
> RCurl_1.95-4.1
>   [9] RSQLite_0.11.4         rtracklayer_1.22.0     stats4_3.0.2
> tools_3.0.2
> [13] XML_3.98-1.1           zlibbioc_1.8.0
>
> thanks!
> robert.
>


-- 
Valerie Obenchain

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B155
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: vobencha at fhcrc.org
Phone:  (206) 667-3158
Fax:    (206) 667-1319