Actually, your 'subjectSet' had non-constant width.  This caused  
trimLRPatterns (any version
from Bioconductor!) for an Rpattern to reverse everything and work on  
the left.  This results
in a call to _nedit_for_Proffset (for the indels situation), which  
isn't written yet.  You'll
have the same failure on ANY call for an Lpattern, with with.Lindels  
TRUE, regardless of the
subject widths.  If your subjectSet had had constant width, the call  
below for the Rpattern
would have worked fine.

The version of mine that I alluded to avoids Proffset, but it has  
slightly different results:

	... demands that matches-with-indels start at the beginning
	of the subject, for Lpattern, and end at the end of the subject, for  
Rpattern.

I think this follows the "spec" (and that the current version does  
not), but others might not
agree or like my results.  I'll submit a patch, along with a laundry  
list of cases.

On Jan 27, 2010, at 4:27 PM, Marcus Davy wrote:
> the arg 'with.Rindels' functionality in trimLRPatterns is not in  
> the current stable release of Bioconductor 2.5, you need to install  
> the development version

 > trimLRPatterns(Rpattern=reverse(pattern),subject=reverse 
(subjectSet),max.Rmismatch=rep(1,nchar(pattern)), with.Rindels=TRUE)
Error in .matchPatternAt(pattern, subject, ending.at, 1L,  
max.mismatch,  :
   _nedit_for_Proffset() is not ready yet, sorry!
 >


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