synchronizeReadDir error

[vincent-hanlon]

Hi David,

I'm trying out the inversion-aware phasing you describe here, which I believe requires using the GitHub master branch of BreakpointR rather than the Bioconductor version. When I use the Bioconductor version, StrandPhaseR gives an error which I won't go into here.

Using the current GitHub version of BreakpointR, I run these commands:
breakpointr(inputfolder="./", outputfolder="./BPR_output_new", numCPU=18, chromosomes=c("chr1","chr7","chr8","chr16"), windowsize=1000000, binMethod="size", pairedEndReads=TRUE)
test <- breakpointR::synchronizeReadDir(list.files("BPR_output_new/data/", full.names=TRUE))

This is gives me the following error:

Error in validObject(ans) : invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical

The origin of this error is this line:

WWandCC.regions.grl <- S4Vectors::endoapply(test, function(x) removeDoubleSCEs(x, collapseWidth = 5000000))

Is there a way to use these tools that avoids this error? Thanks

[daewoooo]

I have just tested this function for breakpointR version 1.13.3 and everything seems to be working fine. Can I get some test dataset from you so I can reproduce the error on my side??? I'm using GenomicRanges version 1.46.

[vincent-hanlon]

Hmm, odd. I am using the same GenomicRanges and BreakpointR versions (see below). I just replicated it again with a smaller set of just three BAM files (data originally from this FTP). I'll send you the three BAM files via Google Drive or something so you can use exactly the same ones.

sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/vhanlon/miniconda2/envs/spr_silly/lib/libopenblasp-r0.3.18.so

locale:
[1] C

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] breakpointR_1.13.3 breakpointRdata_1.12.0 cowplot_1.1.1
[4] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0
[7] S4Vectors_0.32.3 BiocGenerics_0.40.0

loaded via a namespace (and not attached):
[1] compiler_4.1.2 pillar_1.7.0
[3] XVector_0.34.0 MatrixGenerics_1.6.0
[5] iterators_1.0.14 bitops_1.0-7
[7] tools_4.1.2 zlibbioc_1.40.0
[9] digest_0.6.29 lattice_0.20-45
[11] lifecycle_1.0.1 tibble_3.1.6
[13] gtable_0.3.0 pkgconfig_2.0.3
[15] rlang_1.0.1 Matrix_1.4-0
[17] foreach_1.5.2 DelayedArray_0.20.0
[19] cli_3.2.0 DBI_1.1.2
[21] parallel_4.1.2 GenomeInfoDbData_1.2.7
[23] dplyr_1.0.8 gtools_3.9.2
[25] Biostrings_2.62.0 generics_0.1.2
[27] vctrs_0.3.8 grid_4.1.2
[29] tidyselect_1.1.2 Biobase_2.54.0
[31] glue_1.6.2 R6_2.5.1
[33] fansi_1.0.2 BiocParallel_1.28.3
[35] farver_2.1.0 ggplot2_3.3.5
[37] purrr_0.3.4 magrittr_2.0.2
[39] Rsamtools_2.10.0 matrixStats_0.61.0
[41] GenomicAlignments_1.30.0 codetools_0.2-18
[43] scales_1.1.1 ellipsis_0.3.2
[45] SummarizedExperiment_1.24.0 assertthat_0.2.1
[47] colorspace_2.0-3 labeling_0.4.2
[49] utf8_1.2.2 doParallel_1.0.17
[51] RCurl_1.98-1.6 munsell_0.5.0
[53] crayon_1.5.0

[daewoooo]

This issue seems to be restricted to R version 4.1.2. This issue will be investigated further!!!