[BioC] VariantAnnotation updated - error in predictCoding

[bnorthoff at web.de]

   Hi there, i am a bit confused concerning the varAllele by using GRanges:

   snp1  = GRanges(seqnames="chr2", ranges=IRanges(start=28920, width=1),
   refAllele=DNAStringSet("G"), varAllele=DNAStringSet("A"))
   library(TxDb.Mmusculus.UCSC.mm9.knownGene)
   txdb = TxDb.Mmusculus.UCSC.mm9.knownGene
   coding = predictCoding(query=snp1, subject=txdb, seqSource=Mmusculus)

   I thought the varAllele was given by the GRanges, isn't it?


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