May be able to knock out the ambiguous code matching with Biostrings::vmatchPattern(), using the fixed = FALSE or "subject" options (TRUE is default which won't allow for ambiguous matching).
There should be a performance increase with the switch from pairwiseAlignment() to vmatchPattern(), but may not be much.
Biostrings::vmatchPattern() is better suited for the task than pairwiseAlignment, though both can be used.
May be able to knock out the ambiguous code matching with Biostrings::vmatchPattern(), using the fixed = FALSE or "subject" options (TRUE is default which won't allow for ambiguous matching).
There should be a performance increase with the switch from pairwiseAlignment() to vmatchPattern(), but may not be much.
Biostrings::vmatchPattern() is better suited for the task than pairwiseAlignment, though both can be used.