readVcfStack(param=ScanVcfParam()) doesn't work if "which=" is not specified.

Bắt đầu bằng cách tái hiện ví dụ GenomicFiles và VariantAnnotation được cung cấp, so sánh readVcfStack(rstack, param = ScanVcfParam()) với workaround rowRanges và lệnh gọi readVcf đang hoạt động. Truy vết các entry point của readVcfStack và ScanVcfParam để xác định cách xử lý khác nhau đối với giá trị which không được chỉ định. Hoàn tất khi lệnh gọi readVcfStack có tham số hoạt động mà không cần which= và một regression test bao phủ trường hợp này.

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