[Bioc-devel] vmatchPattern Returns Out of Bounds Indices

[Dario Strbenac]

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

This is utilising Biostrings 2.42.0 in R 3.3.1.

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia