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

[Jialin Ma]

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