[Bioc-devel] bamFlagAsBitMatrix error (?bug)

[Valerie Obenchain]

Hi Sean,

Yes, we are aware of the problem, thanks. Hopefully this will be 
resolved for tomorrows builds ... we'll post back when it's fixed.

Val

On 12/14/2014 08:33 AM, Sean Davis wrote:
> Hi, Martin, Val, and Herve.
>
> This looks like a little problem with the bitnames in
> Rsamtools/GenomicAlignments.  Perhaps this is related to some bitnames
> being deprecated?
>
> Thanks,
> Sean
>
>
>> library(GenomicAlignments)
>> sbp = ScanBamParam(which=cds[1:100],flag=scanBamFlag(isDuplicate = FALSE))
>> x = readGAlignmentPairs(LOCALBAMS[180],param=sbp)
> Error in bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead") :
>    invalid bitname(s): isNotPrimaryRead
>> traceback()
> 8: stop("invalid bitname(s): ", in1string)
> 7: bamFlagAsBitMatrix(flag1, bitnames = "isNotPrimaryRead")
> 6: .make_GAlignmentPairs_from_GAlignments(gal, use.mcols = use.mcols)
> 5: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
>         param = param, with.which_label = with.which_label)
> 4: readGAlignmentPairsFromBam(bam, character(), use.names = use.names,
>         param = param, with.which_label = with.which_label)
> 3: readGAlignmentPairsFromBam(file = file, use.names = use.names,
>         ...)
> 2: readGAlignmentPairsFromBam(file = file, use.names = use.names,
>         ...)
> 1: readGAlignmentPairs(LOCALBAMS[180], param = sbp)
>> sessionInfo()
> R Under development (unstable) (2014-11-18 r66997)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices datasets  utils
> methods   base
>
> other attached packages:
>   [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.7
>           AnnotationDbi_1.29.11
>   [4] GenomicAlignments_1.3.14                stringr_0.6.2
>            plotrix_3.5-10
>   [7] pd.huex.1.0.st.v2_3.10.0                RSQLite_1.0.0
>            DBI_0.3.1
> [10] limma_3.23.2                            oligo_1.31.0
>           Biobase_2.27.0
> [13] oligoClasses_1.29.3                     knitr_1.8
>            VariantAnnotation_1.13.19
> [16] Rsamtools_1.19.15                       Biostrings_2.35.7
>            XVector_0.7.3
> [19] GenomicRanges_1.19.21                   GenomeInfoDb_1.3.7
>           IRanges_2.1.33
> [22] S4Vectors_0.5.14                        BiocGenerics_0.13.3
>            BiocInstaller_1.17.1
>
> loaded via a namespace (and not attached):
>   [1] BBmisc_1.8            BSgenome_1.35.8       BatchJobs_1.5
> BiocParallel_1.1.9    RCurl_1.95-4.5        XML_3.98-1.1
>   [7] affxparser_1.39.3-1   affyio_1.35.0         base64enc_0.1-2
> biomaRt_2.23.5        bit_1.1-12            bitops_1.0-6
> [13] brew_1.0-6            checkmate_1.5.1       codetools_0.2-9
> digest_0.6.6          evaluate_0.5.5        fail_1.2
> [19] ff_2.2-13             foreach_1.4.2         formatR_1.0
> htmltools_0.2.6       iterators_1.0.7       knitrBootstrap_1.0.0
> [25] markdown_0.7.4        preprocessCore_1.29.0 rmarkdown_0.3.3
> rtracklayer_1.27.6    sendmailR_1.2-1       splines_3.2.0
> [31] tools_3.2.0           yaml_2.1.13           zlibbioc_1.13.0
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>