[Bioc-devel] rtracklayer::liftOver bug when lifting over few ranges

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Apr 20 22:46:06 CEST 2012

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 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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