[BioC] mismatch nb in Biostrings

[Harris A. Jaffee]

First, see ?`lowlevel-matching`, and if you are really adventurous, the function
nedit_at() in Biostrings/src/lowlevel_matching.c.  The degree to which your pattern
and subjects disagree, in a sense dictated by your with.indels=FALSE and fixed=TRUE
arguments, is determined first, although actually only up to your max.mismatch limit.
Then that (modified) “distance" is tested against your min.mismatch constraint, as it
says here:

     ‘isMatchingAt’: If ‘subject’ is an XString object, then return the
     logical vector defined by:

         min.mismatch <= neditAt(...) <= max.mismatch


On Jul 7, 2014, at 4:37 AM, carol white <wht_crl at yahoo.com> wrote:

> Hi,
> How does it work with mismatch.min, mismatch.max in the functions of Biostrings for ex, vcountPattern? If mismatch.min=0, mismatch.max=2, then if there is no match, the function searches up to 2 matches, that is, if it find matches with 1mismatch, then it searches in the pattern in the next subject, otherwise it tries to find 2 matches in the same subject?
> 
> Look forward to your reply,
> 
> Carol
> 	[[alternative HTML version deleted]]
> 
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