proActiv throws error with xz-compressed Tophat2 junction file

[jleechung]

proActiv throws an error if input file is a xz-compressed TopHat2 junction BED file (.bed.xz). This behaviour stems from readTopHatJunctions (GenomicAlignments package).

> readTopHatJunctions('../sample1.bed.xz')
Error in validObject(.Object) : 
  invalid class “BEDFile” object: invalid object for slot "resource" in class "BEDFile": got class "xzfile", should be or extend class "characterORconnection"
In addition: Warning message:
In readTopHatJunctions("../junction-files/sample3.bed.xz") :
  'file' has no .bed extension, suggesting it may not be a junctions.bed
  file as generated by TopHat. I will assume it is this file anyway (or a BED
  file with similar content). If 'file' is a tab-delimited file obtained
  by running TopHat's bed_to_juncs script on a junctions.bed file, you
  should use 'file.is.raw.juncs=TRUE'

Session info:

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=English_Singapore.1252  LC_CTYPE=English_Singapore.1252    LC_MONETARY=English_Singapore.1252
[4] LC_NUMERIC=C                       LC_TIME=English_Singapore.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GenomicAlignments_1.24.0    Rsamtools_2.4.0             Biostrings_2.56.0           XVector_0.28.0             
 [5] SummarizedExperiment_1.18.1 DelayedArray_0.14.0         matrixStats_0.56.0          Biobase_2.48.0             
 [9] GenomicRanges_1.40.0        GenomeInfoDb_1.24.2         IRanges_2.22.2              S4Vectors_0.26.1           
[13] BiocGenerics_0.34.0        

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11        zlibbioc_1.34.0        BiocParallel_1.22.0    lattice_0.20-41        tools_4.0.0           
 [6] grid_4.0.0             crayon_1.3.4           Matrix_1.2-18          GenomeInfoDbData_1.2.3 rtracklayer_1.48.0    
[11] bitops_1.0-6           RCurl_1.98-1.2         compiler_4.0.0         XML_3.99-0.3