[BioC] unpackVcf not found

[Valerie Obenchain]

Hi Seth,

The .unpackVcf* functions are still there but they aren't (never have 
been) exported. You need to use ::: to get at them.

     VariantAnnotation:::.unpackVcf

readVcf() is much more direct if a VCF object is your end goal.

Valerie

On 01/29/2013 08:04 AM, seth redmond wrote:
> I have some old code that's stopped working since I upgraded to R2.15 due to the unpackVcf method not being found. Is this still in the devel branch? or has it been deprecated completely?
>
> Or does anyone know another workaround I can use?
>
> thanks
>
> -s
>
>
>
>
>>    vcfScan<- scanVcf(file_name)
> There were 50 or more warnings (use warnings() to see the first 50)
>>    scanVcfHeader(file_name)
> class: VCFHeader
> samples(3): Fd03_high.vcf Fd03_low.vcf Fd03_zero.vcf
> meta(2): fileformat samtoolsVersion
> fixed(0):
> info(21): DP DP4 ... AC AN
> geno(7): DP4 GT ... SP PL
>>    vcf<- unpackVcf(vcfScan, vcftab, info=TRUE, geno=TRUE)
> Error: could not find function "unpackVcf"
>>    sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/en_US.UTF-8/C/C/C/C
>
> attached base packages:
>   [1] splines   stats4    grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] VariantAnnotation_1.4.7 GGtools_4.6.2           GGBase_3.20.0           snpStats_1.8.1          Matrix_1.0-10
>   [6] survival_2.37-2         ShortRead_1.16.3        latticeExtra_0.6-24     RColorBrewer_1.0-5      Rsamtools_1.10.2
> [11] lattice_0.20-13         Biostrings_2.26.3       gridExtra_0.9.1         zoo_1.7-9               plyr_1.8
> [16] rtracklayer_1.18.2      GenomicRanges_1.10.6    IRanges_1.16.4          BiocGenerics_0.4.0      ggbio_1.6.6
> [21] ggplot2_0.9.3           BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
>   [1] AnnotationDbi_1.20.3   BSgenome_1.26.1        Biobase_2.18.0         DBI_0.2-5              GenomicFeatures_1.10.1
>   [6] Hmisc_3.10-1           MASS_7.3-23            RCurl_1.95-3           RSQLite_0.11.2         XML_3.95-0.1
> [11] annotate_1.36.0        biomaRt_2.14.0         biovizBase_1.6.2       bit_1.1-9              bitops_1.0-4.2
> [16] cluster_1.14.3         colorspace_1.2-1       dichromat_2.0-0        digest_0.6.1           ff_2.2-10
> [21] genefilter_1.40.0      gtable_0.1.2           hwriter_1.3            labeling_0.1           munsell_0.4
> [26] parallel_2.15.2        proto_0.3-10           reshape2_1.2.2         scales_0.2.3           stringr_0.6.2
> [31] tools_2.15.2           xtable_1.7-0           zlibbioc_1.4.0
>
>
> --
> Seth Redmond
>    Unité Génetique et Génomique des Insectes Vecteurs
>    Institut Pasteur
>    28,rue du Dr Roux
>    75724 PARIS
> seth.redmond at pasteur.fr
>
>
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>
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