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

[Ou, Jianhong]

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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