Implement advanced primer search filtering and reference handling

This update introduces new configuration options for pair selection, including multi-match filtering, circularity settings, and reference site validation. It also enhances the search functionality to correctly identify and track repeated sequences and reference locations, improving the accuracy of primer pair identification.

cmd/obitools/obiprimers/main.go

@@ -35,7 +35,7 @@ func main() {
 		log.Fatalf("%v", err)
 	}
 
-	obicsv.CLICSVWriter(obiprimers.PairsToCSVIterator(pairs), true)
+	obicsv.CLICSVWriter(obiprimers.PairsToCSVIterator(pairs, obiprimers.CLIReference() != ""), true)
 
 	obiutils.WaitForLastPipe()
 }