[Bioc-devel] bamFlagAsBitMatrix error (?bug)

[Valerie Obenchain]

This should be fixed now (thanks Martin).

We recently deprecated the flag 'isNotPrimaryRead' in favor of 
'isNotPrimaryAlignment' (Rsamtools devel). This affected 
GenomicAlignments and others ...

~/b/Rpacks$ grep -lr isNotPrimaryRead *
CoverageView/R/cov.matrix.R
CoverageView/R/cov.interval.R
gage/vignettes/RNA-seqWorkflow.Rnw
hiReadsProcessor/R/hiReadsProcessor.R
QDNAseq/man/binReadCounts.Rd
QDNAseq/R/binReadCounts.R
Rsamtools/NEWS
Rsamtools/man/ScanBamParam-class.Rd
Rsamtools/R/methods-ScanBamParam.R
SplicingGraphs/inst/unitTests/test_countReads-methods.R
SplicingGraphs/inst/scripts/TSPC-utils.R
SplicingGraphs/vignettes/SplicingGraphs.Rnw
SplicingGraphs/man/assignReads.Rd
SplicingGraphs/man/txpath-methods.Rd
systemPipeR/R/utilities.R


These packages should be clear (of this error) on tomorrow's builds.

Thanks.
Val

On 12/14/2014 09:15 AM, Valerie Obenchain wrote:
> 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]]
>>
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