On 11/18/2016 02:00 AM, Dario Strbenac wrote:
Good day,
These questions really belong to the support site.
I suppose, although it seemed like an unexpected issue at first because it's
not documented within ?lowlevel-matching so users don't know what to expect.
You'll get that behaviour by allowing indels.
This reveals a discrepancy between the documentation and the way the function
operates. In the documentation, the function definition of vmatchPattern has
with.indels = FALSE in it. However, changing it to TRUE results in
Error in .XStringSet.vmatchPattern(pattern, subject, max.mismatch,
min.mismatch, :
vmatchPattern() does not support indels yet
Ah ok, right. I tested with matchPattern() only (which does support
indels) and forgot that vmatchPattern() doesn't support them yet.
So I guess a solution for you now is to use one of the 2 other
alternatives i.e. (1) to get rid of the out of bounds matches
or (2) to trim the matches.
H.
This is utilising Biostrings 2.42.0 in R 3.3.1.
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
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Fax: (206) 667-1319
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