[Bioc-devel] bamFlagAsBitMatrix error (?bug)

[Sean Davis]

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]]