[Bioc-devel] "index" option of filterVcf in VariantAnnotation package

[Obenchain, Valerie]

Hi,

Thanks for reporting this.

Now fixed in VariantAnnotaion 1.28.5 (release) and 1.29.11 (devel). 
These version are available immediately from the git server or tomorrow 
after 2pm EST with BiocManager::install().

Valerie




On 12/27/18 10:49 AM, Jialin Ma wrote:
> 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
> 
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 



This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.