Thanks Steve. Sorry for the late response. I committed (for 1.17.6) a
possible fix that is is a variant of your patch. Just passes drop=TRUE to
the split().

Please let me know if it works.

Thanks,
Michael

On Fri, Apr 20, 2012 at 1:46 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi Michael and devs,
>
> Lifting over a GRanges object w/ just one (and I assume only a few)
> ranges causes rtracklayer to complain w/ the following message:
>
> Error in unlist(mseqapply(liftOverSpace, rl[sharedNames],
> chain[sharedNames],  :
>  error in evaluating the argument 'x' in selecting a method for
> function 'unlist': Error in seqnames(gr)[1] :
>  subscript contains NAs or out of bounds indices
>
> It seems that removing seqnames from `rl` that aren't in the `x`
> argument of the liftOver call fixes the stuff. I did this by adding
> the following line after line 103 in chain.R:
>
> rl <- split(x, seqnames(x))  ## This is line 103
> rl <- rl[as.logical(seqapply(rl, length) > 0)]  ## This is the line I added
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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