[Bioc-devel] vmatchPattern Returns Out of Bounds Indices
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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