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.

pkg/obiprimer/pairs.go

@@ -22,6 +22,8 @@ type PairParams struct {
 	FalsePositive  float64 // -x: and less than this fraction of the counterexamples (0.1)
 	MinSpecificity float64 // -T: pairs with a lower Bs are dropped (0.6)
 	Circular       bool    // -c
+	Reference      int     // -R: corpus index of the reference sequence (used when HasReference)
+	HasReference   bool
 }
 
 func (p PairParams) validate() error {