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Bioconductor / VariantAnnotation

Annotation of Genetic Variants
https://bioconductor.org/packages/VariantAnnotation
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readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified. #50

Open Liubuntu opened 2 years ago

Liubuntu commented 2 years ago

As the title indicates, I have to add "which=rowRanges()" to make the readVcfStack work when using param. readVcf works as expected. Issue only exist in Bioc devel. Coding in bioc devel docker. 

library(VariantAnnotation)

extdata <- system.file(package="GenomicFiles", "extdata")
files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)
names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))
seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")

stack <- VcfStack(files, seqinfo)
rstack <- RangedVcfStack(stack)

readVcfStack(rstack)  ## works                                                                                                                                                                                 
readVcfStack(rstack, param = ScanVcfParam())  ## doesn't work                                                                                                                                                  
readVcfStack(rstack, param = ScanVcfParam(which = rowRanges(rstack))) ## workaround                                                                                            

?ScanVcfParam
## which: ... If ‘which’ is not specified all ranges are returned.                                                                                                                                             

## readVcf
vf <- VcfFile(files[1])
readVcf(vf, "hg19")
readVcf(vf, "hg19", param = ScanVcfParam())  ## works

sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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 stats graphics grDevices utils datasets methods [8] base

other attached packages: [1] GenomicFiles_1.29.0 rtracklayer_1.53.1 [3] BiocParallel_1.27.12 VariantAnnotation_1.39.0 [5] Rsamtools_2.9.1 Biostrings_2.61.2 [7] XVector_0.33.0 SummarizedExperiment_1.23.4 [9] Biobase_2.53.0 GenomicRanges_1.45.0 [11] GenomeInfoDb_1.29.8 IRanges_2.27.2 [13] S4Vectors_0.31.5 MatrixGenerics_1.5.4 [15] matrixStats_0.61.0 BiocGenerics_0.39.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.7 lattice_0.20-45 prettyunits_1.1.1 [4] png_0.1-7 assertthat_0.2.1 digest_0.6.28 [7] utf8_1.2.2 BiocFileCache_2.1.1 R6_2.5.1 [10] RSQLite_2.2.8 httr_1.4.2 pillar_1.6.3 [13] zlibbioc_1.39.0 rlang_0.4.11 GenomicFeatures_1.45.2 [16] progress_1.2.2 curl_4.3.2 rstudioapi_0.13 [19] blob_1.2.2 Matrix_1.3-4 stringr_1.4.0 [22] RCurl_1.98-1.5 bit_4.0.4 biomaRt_2.49.4 [25] DelayedArray_0.19.4 compiler_4.1.1 pkgconfig_2.0.3 [28] tidyselect_1.1.1 KEGGREST_1.33.0 tibble_3.1.4 [31] GenomeInfoDbData_1.2.7 XML_3.99-0.8 fansi_0.5.0 [34] crayon_1.4.1 dplyr_1.0.7 dbplyr_2.1.1 [37] GenomicAlignments_1.29.0 bitops_1.0-7 rappdirs_0.3.3 [40] grid_4.1.1 lifecycle_1.0.1 DBI_1.1.1 [43] magrittr_2.0.1 stringi_1.7.4 cachem_1.0.6 [46] xml2_1.3.2 ellipsis_0.3.2 filelock_1.0.2 [49] vctrs_0.3.8 generics_0.1.0 rjson_0.2.20 [52] restfulr_0.0.13 tools_4.1.1 bit64_4.0.5 [55] BSgenome_1.61.0 glue_1.4.2 purrr_0.3.4 [58] hms_1.1.1 yaml_2.2.1 parallel_4.1.1 [61] fastmap_1.1.0 AnnotationDbi_1.55.1 memoise_2.0.0 [64] BiocIO_1.3.0