I would like to cache bam files and their index files using BiocFileCache. However the prefixes added to filenames in the cache can prevent downstream tools from recognizing the index. Is there a way to have the same prefix for files in a BiocFileCache?

library(Rsamtools)
library(BiocFileCache)

bam_fn <- system.file("extdata", "ex1.bam", package="Rsamtools",
                  mustWork=TRUE)
idx_fn <- indexBam(bam_fn)

tmpdir <- tempdir()
on.exit(unlink(tmpdir))

bfc <- BiocFileCache(tmpdir)
bid <- bfcadd(bfc, bam_fn)
iid <- bfcadd(bfc, idx_fn)
bid
#>                                                                                 BFC1 
#> "/var/folders/r9/g3c47jrj40gc14d8qsqx7src0000gn/T//RtmpZBmvJe/14178762f5e8e_ex1.bam"
iid
#>                                                                                     BFC2 
#> "/var/folders/r9/g3c47jrj40gc14d8qsqx7src0000gn/T//RtmpZBmvJe/141781fe8f940_ex1.bam.bai"

It is now possible to override the unique identifier addition. Unique identifiers are still the default. See https://github.com/Bioconductor/BiocFileCache/issues/40

Currently, no there is not a way to disable it automatically but based on the current example it seems desirable to turn off this feature on occasion. I will open an issue on BiocFileCache for an option to disable opened issued. I think people have temporarily gotten around this by creating a local symlink after the files have been cached (granted not ideal but a temporary fix will we work on the feature request)

I assume this is using local files just for reproducibility but if not than another option would be to use the "local" option for caching existing files (but there would be no check for auto updates of the remote file if associated with some remote).

> library(BiocFileCache)
Loading required package: dbplyr
> 
> bam_fn <- system.file("extdata", "ex1.bam", package="Rsamtools",
+                   mustWork=TRUE)
> idx_fn <- indexBam(bam_fn)
> tmpdir <- tempdir()
> bfc <- BiocFileCache(tmpdir)
> bfcadd(bfc, bam_fn, rtype="local", action="asis")
                                                               BFC1 
"/home/shepherd/R-Libraries/4.2-Bioc3.16/Rsamtools/extdata/ex1.bam"