[Bioc-devel] VariantAnnotation::readVcf() sets the wrong seqlevelsStyle in devel

[Robert Castelo]

hi,

it looks like either VariantAnnotation::readVcf() or something in the 
CollapsedVCF class broke in devel with respect to reading and setting 
sequence styles:

library(VariantAnnotation)

fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
seqlevels(vcf)
[1] "22"
seqlevelsStyle(vcf)
[1] "UCSC"
seqlevelsStyle(vcf) <- "UCSC"
seqlevels(vcf)
[1] "22"

you can find my session information below. let me know if you want me to 
open an issue at the GitHub repo (VariantAnnotatoin or GenomeInfoDb?).

thanks!

robert.

BiocManager::version()
[1] ‘3.12’
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] VariantAnnotation_1.35.3 Rsamtools_2.5.3
  [3] Biostrings_2.57.2 XVector_0.29.3
  [5] SummarizedExperiment_1.19.6 DelayedArray_0.15.7
  [7] matrixStats_0.56.0 Matrix_1.2-18
  [9] Biobase_2.49.0 GenomicRanges_1.41.5
[11] GenomeInfoDb_1.25.8 IRanges_2.23.10
[13] S4Vectors_0.27.12 BiocGenerics_0.35.4
[15] BiocManager_1.30.10

loaded via a namespace (and not attached):
  [1] progress_1.2.2           tidyselect_1.1.0 purrr_0.3.4
  [4] lattice_0.20-41          vctrs_0.3.1 generics_0.0.2
  [7] BiocFileCache_1.13.0     rtracklayer_1.49.4 GenomicFeatures_1.41.2
[10] blob_1.2.1               XML_3.99-0.4 rlang_0.4.6
[13] pillar_1.4.4             glue_1.4.1 DBI_1.1.0
[16] rappdirs_0.3.1           BiocParallel_1.23.2 bit64_0.9-7.1
[19] dbplyr_1.4.4             GenomeInfoDbData_1.2.3 lifecycle_0.2.0
[22] stringr_1.4.0            zlibbioc_1.35.0 memoise_1.1.0
[25] biomaRt_2.45.2           curl_4.3 AnnotationDbi_1.51.3
[28] Rcpp_1.0.4.6             BSgenome_1.57.5 openssl_1.4.1
[31] bit_1.1-15.2             hms_0.5.3 askpass_1.1
[34] digest_0.6.25            stringi_1.4.6 dplyr_1.0.0
[37] grid_4.0.0               tools_4.0.0 bitops_1.0-6
[40] magrittr_1.5             RCurl_1.98-1.2 RSQLite_2.2.0
[43] tibble_3.0.1             crayon_1.3.4 pkgconfig_2.0.3
[46] ellipsis_0.3.1           prettyunits_1.1.1 assertthat_0.2.1
[49] httr_1.4.1               R6_2.4.1 GenomicAlignments_1.25.3
[52] compiler_4.0.0