fix: respect config defaults when --allowed-mismatches is unset

The change replaces numeric threshold checks with an explicit flag state tracker for the `--allowed-mismatches` option. This ensures per-primer mismatch settings from configuration files are preserved when the CLI parameter is omitted or zero, making the command-line flag act strictly as an explicit override rather than a default fallback.

pkg/obingslibrary/multimatch.go

@@ -777,7 +777,7 @@ func (library *NGSLibrary) ExtractMultiBarcodeSliceWorker(options ...WithOption)
 		library.SetAllowsIndels(true)
 	}
 
-	if opt.AllowedMismatches() > 0 {
+	if opt.AllowedMismatchesIsSet() {
 		library.SetAllowedMismatches(opt.AllowedMismatches())
 	}
 

pkg/obingslibrary/worker.go

@@ -6,13 +6,14 @@ import (
 )
 
 type _Options struct {
-	discardErrors   bool
-	unidentified    string
-	allowedMismatch int
-	allowsIndel     bool
-	withProgressBar bool
-	parallelWorkers int
-	batchSize       int
+	discardErrors      bool
+	unidentified       string
+	allowedMismatch    int
+	allowedMismatchSet bool
+	allowsIndel        bool
+	withProgressBar    bool
+	parallelWorkers    int
+	batchSize          int
 }
 
 // Options stores a set of option usable by the
@@ -52,6 +53,7 @@ func OptionWithProgressBar(yes bool) WithOption {
 func OptionAllowedMismatches(count int) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.allowedMismatch = count
+		opt.pointer.allowedMismatchSet = true
 	})
 
 	return f
@@ -97,6 +99,12 @@ func (options Options) AllowedMismatches() int {
 	return options.pointer.allowedMismatch
 }
 
+// AllowedMismatchesIsSet returns true if OptionAllowedMismatches
+// was explicitly applied to these options.
+func (options Options) AllowedMismatchesIsSet() bool {
+	return options.pointer.allowedMismatchSet
+}
+
 func (options Options) AllowsIndels() bool {
 	return options.pointer.allowsIndel
 }