[BioC] Rsamtools Package Dereferences Symbolic Links

Cook, Malcolm MEC at stowers.org
Tue Oct 16 17:00:00 CEST 2012


I too have noticed this.  Further, consistently with this, if you use the
Rsamtools package to create the indices to symlinks pointing to bamfiles,
the indices are created in the target directory.

I think if there is a code change to address this issue by allowing
control over whether links are dereferenced, the DEFAULT should be NOT to
dereference like this.

--Malcolm Cook

On 10/15/12 9:24 PM, "Lucas Swanson" <lswanson at bcgsc.ca> wrote:

>I am attempting to use your Rsamtools Bioconductor package.
>Unfortunately, I am having a bit of trouble. You see, my BAM files are in
>a directory to which I do not have write access, and are too large for me
>to copy to my own directory. So I created symbolic links in my own
>directory, pointing to the BAM files, and then indexed them in my own
>directory. However, when I try to use these symbolic links the Rsamtools
>package dereferences the links, and looks for the indexes in the original
>directory (to which I do not have write access), rather than in my own
>Is there any way to prevent Rsamtools from dereferencing symbolic links?
>(That is, not replacing paths to symbolic links with paths to the target
>of the link)
>~Thank you,
>Lucas Swanson
>Bioconductor mailing list
>Bioconductor at r-project.org
>Search the archives:

More information about the Bioconductor mailing list