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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