[Bioc-devel] a possible bug in development version of GenomicAlignments

[Hervé Pagès]

Hi Jianhong,

Thanks for catching and reporting this. Should be fixed in
GenomicAlignments 1.15.2:

 
https://github.com/Bioconductor/GenomicAlignments/commit/aa6a7d2ad6c75595127e96ae1b924b58608b8da5

Cheers,
H.


On 11/30/2017 03:40 PM, Ou, Jianhong wrote:
> Hi, is this a bug in the development version of GenomicAlignments or compressedList? Or I missed anything?
>
> Here is how to repeat the error:
>
>
>> library(GenomicAlignments)
>
>> gal1 <- GAlignments(
>
> +     seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
>
> +         c(1, 3, 2, 4)),
>
> +     pos=1:10, cigar=paste0(10:1, "M"),
>
> +     strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
>
> +     names=head(letters, 10), score=1:10)
>
>>
>
>> gal2 <- GAlignments(
>
> +     seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
>
> +     cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
>
> +     strand=Rle(strand(c("-", "+")), c(4, 3)),
>
> +     names=tail(letters, 7), score=1:7)
>
>>
>
>> galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
>
>> galist[["Gaps"]] <- gal2
>
> Error in .wrap_in_length_one_list_like_object(value, names(x)[[i]], x) :
>
>    failed to coerce 'list(value)' to a GAlignmentsList object of length 1
>
>> sessionInfo()
>
>
> R Under development (unstable) (2017-11-29 r73795)
>
> Platform: x86_64-apple-darwin17.2.0 (64-bit)
>
> Running under: macOS High Sierra 10.13.1
>
>
> Matrix products: default
>
> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib
>
> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
>
>
> locale:
>
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>
> attached base packages:
>
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>
> [8] methods   base
>
>
> other attached packages:
>
>   [1] GenomicAlignments_1.15.1   Rsamtools_1.31.0
>
>   [3] Biostrings_2.47.0          XVector_0.19.1
>
>   [5] SummarizedExperiment_1.9.2 DelayedArray_0.5.6
>
>   [7] matrixStats_0.52.2         Biobase_2.39.0
>
>   [9] GenomicRanges_1.31.1       GenomeInfoDb_1.15.1
>
> [11] IRanges_2.13.4             S4Vectors_0.17.10
>
> [13] BiocGenerics_0.25.0
>
>
> loaded via a namespace (and not attached):
>
>   [1] lattice_0.20-35         bitops_1.0-6            grid_3.5.0
>
>   [4] zlibbioc_1.25.0         Matrix_1.2-12           BiocParallel_1.13.0
>
>   [7] tools_3.5.0             RCurl_1.95-4.8          compiler_3.5.0
>
> [10] GenomeInfoDbData_0.99.2
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> TEL: 508-856-5379
> LRB 608
> Bioinformatician of Bioinformatics core at
> Department of Molecular, Cell and Cancer Biology
> UMASS Medical School
> 364 Plantation Street Worcester,
> MA 01605
>
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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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