[Bioc-devel] vmatchPattern Returns Out of Bounds Indices

[Hervé Pagès]

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
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
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: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319