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ngsfilter: error arg / fuzzy pattern match - Printable Version

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ngsfilter: error arg / fuzzy pattern match - cbird - 07-23-2016

The documentation states that the -e argument allows one to set the number of allowable errors in the pattern match to the primer.

What errors are included? Insertions, deletions, and substitutions?

If -e 2,  would that allow for 2 "errors" in the pattern match to one primer, or 2 errors across both primers?  

Am I correct in understanding that there can be no errors in the pattern match to the tags?

I can figure it out from here:

https://git.metabarcoding.org/obitools/obitools/blob/master/src/ngsfilter.py


RE: ngsfilter: error arg / fuzzy pattern match - coissac - 07-23-2016

an error is a mismatch or an indel ans -e 2 is 2 error for each primer