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
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