Dear all,
The `index` option of filterVcf function in VariantAnnotation package
currently does not seem to work.
The following is a minimal reproducible example:
??R> vcf <- VcfFile(system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation"))
??R> filterVcf(vcf, destination = tempfile(), index = TRUE, verbose = TRUE,
???????????? prefilters = FilterRules( function(x) rep(TRUE, length(x)) ))
starting prefilter
prefiltering 10376 records
prefiltered to /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b67ce9179
compressing and indexing ?/var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b67ce9179?
Error: 'bgzip' error: opening 'file': No such file or directory
??file: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b67ce9179
??dest: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b721b71d5.bgz'<pointer: 0x11ea398c0>' error: opening 'file': No such file or directory
??file: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b67ce9179
??dest: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b721b71d5.bgz'list(name = "Rsamtools", path = "/Library/Frameworks/Rframework/Versions/3.5/Resources/library/Rsamtools/libs/Rsamtools.so", dynamicLookup = TRUE, handle = <pointer: 0x11fb45f00>, info = <pointer: 0x10286fb00>)' error: opening 'file': No such file or directory
??file: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b67ce9179
??dest: /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b721b71d5.bgz'2' error: opening 'file': No such file or directory
??file: /var/folders/
In contrast, by turning `index` option to FALSE, it will no longer produce any error.
??R> filterVcf(vcf, destination = tempfile(), index = FALSE, verbose = TRUE,
????????????prefilters = FilterRules( function(x) rep(TRUE, length(x)) ))
starting prefilter
prefiltering 10376 records
prefiltered to /var/folders/59/1dny9n9d23jb7xmrh7c6jjc80000gn/T//RtmpoZLcSF/filefd5b3f39ec40
I am not sure whether the name of output file is supposed to have extension such as ".vcf.bgz",
but I have tried both.
Sorry that I haven't switched to devel brunch of Bioconductor. Please help verify the problem.
Thank you!
Jialin
R> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
attached base packages:
[1] stats4????parallel??stats???? graphics??grDevices utils???? datasets?
[8] methods?? base?????
other attached packages:
[1] VariantAnnotation_1.26.1????Rsamtools_1.32.3???????????
[3] Biostrings_2.48.0?????????? XVector_0.20.0?????????????
[5] SummarizedExperiment_1.10.1 DelayedArray_0.6.6?????????
[7] BiocParallel_1.14.2???????? matrixStats_0.54.0?????????
[9] Biobase_2.40.0??????????????GenomicRanges_1.32.7???????
[11] GenomeInfoDb_1.16.0???????? IRanges_2.14.12????????????
[13] S4Vectors_0.18.3????????????BiocGenerics_0.26.0????????
[15] magrittr_1.5???????????????
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0?????????????? compiler_3.5.1??????????
[3] prettyunits_1.0.2????????GenomicFeatures_1.32.3??
[5] bitops_1.0-6???????????? tools_3.5.1?????????????
[7] zlibbioc_1.26.0??????????progress_1.2.0??????????
[9] biomaRt_2.36.1?????????? digest_0.6.18???????????
[11] bit_1.1-14?????????????? BSgenome_1.48.0?????????
[13] RSQLite_2.1.1????????????memoise_1.1.0???????????
[15] lattice_0.20-38??????????pkgconfig_2.0.2?????????
[17] rlang_0.3.0.1????????????Matrix_1.2-15???????????
[19] cli_1.0.1????????????????DBI_1.0.0???????????????
[21] rstudioapi_0.8?????????? yaml_2.2.0??????????????
[23] GenomeInfoDbData_1.1.0?? withr_2.1.2?????????????
[25] rtracklayer_1.40.6?????? httr_1.4.0??????????????
[27] stringr_1.3.1????????????hms_0.4.2???????????????
[29] bit64_0.9-7??????????????grid_3.5.1??????????????
[31] R6_2.3.0???????????????? AnnotationDbi_1.42.1????
[33] XML_3.98-1.16????????????sessioninfo_1.1.1???????
[35] blob_1.1.1?????????????? GenomicAlignments_1.16.0
[37] assertthat_0.2.0???????? stringi_1.2.4???????????
[39] RCurl_1.95-4.11??????????crayon_1.3.4????????????