[Bioc-devel] bamFlagAsBitMatrix error (?bug)

[Hervé Pagès]

Hi,

On 12/14/2014 01:29 PM, Valerie Obenchain wrote:
> This should be fixed now (thanks Martin).
>
> We recently deprecated the flag 'isNotPrimaryRead' in favor of
> 'isNotPrimaryAlignment' (Rsamtools devel).

The new name is actually isSecondaryAlignment.

H.

> 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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>>>
>>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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