[BioC] readVcf fails when ALT field contains breakends and no symbolic allele

[Daniel Cameron]

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    <DEL>    .    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.
>>
>


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