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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