Bug in VRanges conversion in VariantAnnotation (devel)
1
0
Entering edit mode
sidb • 0
@sidb-7853
Last seen 5.7 years ago
United States

I am seeing an error in the devel version of VariantAnnotation for VCF to VRanges conversion after this commit.

> library(VariantAnnotation)
> ​fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> as(vcf, "VRanges")
Error in if allis.na(x)) || all(x == "PASS")) return(FilterMatrix(matrix(nrow = length(x),  : 
  missing value where TRUE/FALSE needed

> traceback()
3: parseFilterStrings(rd$FILTER)
2: asMethod(object)
1: as(vcf, "VRanges")

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     
other attached packages:
 [1] VariantAnnotation_1.19.4   Rsamtools_1.25.0          
 [3] Biostrings_2.41.4          XVector_0.13.2            
 [5] SummarizedExperiment_1.3.6 Biobase_2.33.0            
 [7] GenomicRanges_1.25.8       GenomeInfoDb_1.9.1        
 [9] IRanges_2.7.11             S4Vectors_0.11.7          
[11] BiocGenerics_0.19.1       
loaded via a namespace (and not attached):
 [1] XML_3.98-1.4            GenomicAlignments_1.9.4 bitops_1.0-6           
 [4] DBI_0.4-1               RSQLite_1.0.0           GenomicFeatures_1.25.14
 [7] zlibbioc_1.19.0         BiocParallel_1.7.4      tools_3.3.0            
[10] BSgenome_1.41.2         biomaRt_2.29.2          RCurl_1.95-4.8         
[13] rtracklayer_1.33.8      AnnotationDbi_1.35.3  
VariantAnnotation • 698 views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-3846
Last seen 2.3 years ago
United States

Thanks, should be fixed in 1.19.5.

ADD COMMENT

Login before adding your answer.

Traffic: 602 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6