Refactor k-mer index building to use disk-based KmerSetGroupBuilder

Refactor k-mer index building to use the new disk-based KmerSetGroupBuilder instead of the old KmerSet and FrequencyFilter approaches. This change introduces a more efficient and scalable approach to building k-mer indices by using partitioned disk storage with streaming operations.

- Replace BuildKmerIndex and BuildFrequencyFilterIndex with KmerSetGroupBuilder
- Add support for frequency filtering via WithMinFrequency option
- Remove deprecated k-mer set persistence methods
- Update CLI to use new builder approach
- Add new disk-based k-mer operations (union, intersect, difference, quorum)
- Introduce KDI (K-mer Delta Index) file format for efficient storage
- Add K-way merge operations for combining sorted k-mer streams
- Update documentation and examples to reflect new API

This refactoring provides better memory usage, faster operations on large datasets, and more flexible k-mer set operations.

pkg/obikmer/varint_test.go

@@ -0,0 +1,82 @@
+package obikmer
+
+import (
+	"bytes"
+	"testing"
+)
+
+func TestVarintRoundTrip(t *testing.T) {
+	values := []uint64{
+		0, 1, 127, 128, 255, 256,
+		16383, 16384,
+		1<<21 - 1, 1 << 21,
+		1<<28 - 1, 1 << 28,
+		1<<35 - 1, 1 << 35,
+		1<<42 - 1, 1 << 42,
+		1<<49 - 1, 1 << 49,
+		1<<56 - 1, 1 << 56,
+		1<<63 - 1, 1 << 63,
+		^uint64(0), // max uint64
+	}
+
+	for _, v := range values {
+		var buf bytes.Buffer
+		n, err := EncodeVarint(&buf, v)
+		if err != nil {
+			t.Fatalf("EncodeVarint(%d): %v", v, err)
+		}
+		if n != VarintLen(v) {
+			t.Fatalf("EncodeVarint(%d): wrote %d bytes, VarintLen says %d", v, n, VarintLen(v))
+		}
+
+		decoded, err := DecodeVarint(&buf)
+		if err != nil {
+			t.Fatalf("DecodeVarint for %d: %v", v, err)
+		}
+		if decoded != v {
+			t.Fatalf("roundtrip failed: encoded %d, decoded %d", v, decoded)
+		}
+	}
+}
+
+func TestVarintLen(t *testing.T) {
+	tests := []struct {
+		value    uint64
+		expected int
+	}{
+		{0, 1},
+		{127, 1},
+		{128, 2},
+		{16383, 2},
+		{16384, 3},
+		{^uint64(0), 10},
+	}
+
+	for _, tc := range tests {
+		got := VarintLen(tc.value)
+		if got != tc.expected {
+			t.Errorf("VarintLen(%d) = %d, want %d", tc.value, got, tc.expected)
+		}
+	}
+}
+
+func TestVarintSequence(t *testing.T) {
+	var buf bytes.Buffer
+	values := []uint64{0, 42, 1000000, ^uint64(0), 1}
+
+	for _, v := range values {
+		if _, err := EncodeVarint(&buf, v); err != nil {
+			t.Fatalf("EncodeVarint(%d): %v", v, err)
+		}
+	}
+
+	for _, expected := range values {
+		got, err := DecodeVarint(&buf)
+		if err != nil {
+			t.Fatalf("DecodeVarint: %v", err)
+		}
+		if got != expected {
+			t.Errorf("got %d, want %d", got, expected)
+		}
+	}
+}