No problem. Glad it works for you. Valerie On 11/05/13 20:31, Daniel Cameron wrote: > Works with R 3.0.2 / VariationAnnotation 1.8.2 for both minimal test > case and my actual data. Sincere apologies for the inconvenience caused. > > Regards > Daniel Cameron > > On 6/11/2013 11:25 AM, Valerie Obenchain wrote: >> Hi Daniel, >> >> I can't reproduce this error. >> >> It looks like your version of R and Bioconductor packages are out of >> date. The current R version is 3.0.2 and VariantAnnotation is 1.8.2 >> (release) and 1.9.7 (devel). Help for updating is here, >> >> http://www.bioconductor.org/install/ >> >> Let me know if you get the same error after updating and send a small >> sample file if possible. >> >> Thanks. >> Valerie >> >> >> On 10/24/2013 08:58 PM, Daniel Cameron [guest] wrote: >>> readVcf fails to load VCF files where alternate alleles containing >>> breakends exist but no symbolic alleles. If any variant in the VCF >>> contains a symbolic alleles, then the VCF does load correctly >>> (including any breakend alleles - see example below). >>> >>> >>> Reproduction steps: >>>> library(VariantAnnotation) >>>> readVcf("fail.vcf", "fake.fa") >>> Error in .Call2("new_XString_from_CHARACTER", classname, x, >>> start(solved_SEW), : >>> key 91 (char '[') not in lookup table >>>> readVcf("success.vcf", "fake.fa") >>> >>> fail.vcf: >>> ##fileformat=VCFv4.1 >>> ##INFO=<id=svtype,number=1,type=string,description="type of="">>> structural variant"> >>> ##ALT=<id=del,description="deletion"> >>> #CHROM POS ID REF ALT QUAL FILTER INFO >>> 1 1 ref1 G G[1:2[ . PASS SVTYPE=BND >>> >>> success.vcf: >>> ##fileformat=VCFv4.1 >>> ##INFO=<id=svtype,number=1,type=string,description="type of="">>> structural variant"> >>> ##ALT=<id=del,description="deletion"> >>> #CHROM POS ID REF ALT QUAL FILTER INFO >>> 1 1 ref1 G G[1:2[ . PASS SVTYPE=BND >>> 1 2 ref2 G . PASS SVTYPE=DEL >>> >>> >>> -- output of sessionInfo(): >>> >>> R version 2.15.2 (2012-10-26) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 >>> LC_MONETARY=English_Australia.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] VariantAnnotation_1.4.12 Rsamtools_1.10.2 >>> Biostrings_2.26.3 GenomicRanges_1.10.7 IRanges_1.16.6 >>> [6] BiocGenerics_0.4.0 >>> >>> loaded via a namespace (and not attached): >>> [1] AnnotationDbi_1.20.7 Biobase_2.18.0 biomaRt_2.14.0 >>> bitops_1.0-6 BSgenome_1.26.1 >>> [6] DBI_0.2-7 GenomicFeatures_1.10.2 >>> parallel_2.15.2 RCurl_1.95-4.1 RSQLite_0.11.4 >>> [11] rtracklayer_1.18.2 stats4_2.15.2 tools_2.15.2 >>> XML_3.98-1.1 zlibbioc_1.4.0 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >> > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:6}}