[BioC] intermittent oddity in rtracklayer track names

Paul Shannon pshannon at systemsbiology.org
Mon Oct 25 22:33:44 CEST 2010

I've tried hard to come up with a minimal example of this -- some fragment of code to reproduce the error -- but I haven't figured out yet how to do that.  So instead, and thinking that a brief report might be useful, and will possibly trigger something in Michael's mind, I send this narrative email instead.

I create a track with this command:

   track (session, 'exonHits') = grange   # a GRangesForUCSCGenome object

Then I ask to look at the track:

   view <- browserView (session, range.to.view, full='exonHits', dense='ruler', hide=trackNames (session))

The problem is that sometimes I get this error:

   Error in resolveTrackIndex(x, i) : Unknown track(s): exonHits

When I look for the 'exonHits' track, I learn that there are actually two of them, each with a suffix:  "exonHits m" and "exonHits p"

    > grep ('exonHits',  trackNames (session.sub), ignore.case=T, v=T)
             exonHits m          exonHits p
     "ct_exonHitsm_7841" "ct_exonHitsp_7844"

I can use these odd, modified track names, and display the desired:

   view <- browserView (session, range.to.view, full='exonHits m', dense='ruler', hide=trackNames (session))

But it seems rather suspicious.  Is there any reason for the 'm' and 'p' suffixes?


 - Paul


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