Refactor SuperKmer extraction to use iterator pattern

This commit refactors the SuperKmer extraction functionality to use Go's new iterator pattern. The ExtractSuperKmers function is now implemented as a wrapper around a new IterSuperKmers iterator function, which yields results one at a time instead of building a complete slice. This change provides better memory efficiency and more flexible consumption of super k-mers. The functionality remains the same, but the interface is now more idiomatic and efficient for large datasets.

pkg/obikmer/superkmer_iter_test.go

@@ -0,0 +1,82 @@
+package obikmer
+
+import (
+	"testing"
+)
+
+func TestIterSuperKmers(t *testing.T) {
+	seq := []byte("ACGTACGTGGGGAAAA")
+	k := 5
+	m := 3
+
+	count := 0
+	for sk := range IterSuperKmers(seq, k, m) {
+		count++
+		t.Logf("SuperKmer %d: Minimizer=%d, Start=%d, End=%d, Seq=%s",
+			count, sk.Minimizer, sk.Start, sk.End, string(sk.Sequence))
+
+		// Verify sequence boundaries
+		if sk.Start < 0 || sk.End > len(seq) {
+			t.Errorf("Invalid boundaries: Start=%d, End=%d, seqLen=%d",
+				sk.Start, sk.End, len(seq))
+		}
+
+		// Verify sequence content
+		if string(sk.Sequence) != string(seq[sk.Start:sk.End]) {
+			t.Errorf("Sequence mismatch: expected %s, got %s",
+				string(seq[sk.Start:sk.End]), string(sk.Sequence))
+		}
+	}
+
+	if count == 0 {
+		t.Error("No super k-mers extracted")
+	}
+
+	t.Logf("Total super k-mers extracted: %d", count)
+}
+
+func TestIterSuperKmersVsSlice(t *testing.T) {
+	seq := []byte("ACGTACGTGGGGAAAAACGTACGT")
+	k := 7
+	m := 4
+
+	// Extract using slice version
+	sliceResult := ExtractSuperKmers(seq, k, m, nil)
+
+	// Extract using iterator version
+	var iterResult []SuperKmer
+	for sk := range IterSuperKmers(seq, k, m) {
+		iterResult = append(iterResult, sk)
+	}
+
+	// Compare counts
+	if len(sliceResult) != len(iterResult) {
+		t.Errorf("Different number of super k-mers: slice=%d, iter=%d",
+			len(sliceResult), len(iterResult))
+	}
+
+	// Compare each super k-mer
+	for i := 0; i < len(sliceResult) && i < len(iterResult); i++ {
+		slice := sliceResult[i]
+		iter := iterResult[i]
+
+		if slice.Minimizer != iter.Minimizer {
+			t.Errorf("SuperKmer %d: different minimizers: slice=%d, iter=%d",
+				i, slice.Minimizer, iter.Minimizer)
+		}
+
+		if slice.Start != iter.Start || slice.End != iter.End {
+			t.Errorf("SuperKmer %d: different boundaries: slice=[%d:%d], iter=[%d:%d]",
+				i, slice.Start, slice.End, iter.Start, iter.End)
+		}
+
+		if string(slice.Sequence) != string(iter.Sequence) {
+			t.Errorf("SuperKmer %d: different sequences: slice=%s, iter=%s",
+				i, string(slice.Sequence), string(iter.Sequence))
+		}
+	}
+}
+
+// Note: Tests for ToBioSequence and SuperKmerWorker are in a separate
+// integration test package to avoid circular dependencies between
+// obikmer and obiseq packages.