[BioC] Rsamtools Package Dereferences Symbolic Links

[Lucas Swanson]

Hello,

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 directory.

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