mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
f78543ee75
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.
83 lines
1.6 KiB
Go
83 lines
1.6 KiB
Go
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)
|
|
}
|
|
}
|
|
}
|