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https://github.com/metabarcoding/obitools4.git
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Refactor k-mer normalization functions and add quorum operations
This commit refactors the k-mer normalization functions, renaming them from 'NormalizeKmer' to 'CanonicalKmer' to better reflect their purpose of returning canonical k-mers. It also introduces new quorum operations (AtLeast, AtMost, Exactly) for k-mer set groups, along with comprehensive tests and benchmarks. The version commit hash has also been updated.
This commit is contained in:
Eric Coissac
395
pkg/obikmer/kmer_set_group_quorum_test.go
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395
pkg/obikmer/kmer_set_group_quorum_test.go
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package obikmer
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import (
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"testing"
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)
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// TestQuorumAtLeastEdgeCases tests edge cases for QuorumAtLeast
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func TestQuorumAtLeastEdgeCases(t *testing.T) {
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k := 5
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// Test group with all empty sets
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emptyGroup := NewKmerSetGroup(k, 3)
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result := emptyGroup.QuorumAtLeast(1)
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if result.Len() != 0 {
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t.Errorf("Empty sets: expected 0 k-mers, got %d", result.Len())
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}
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// Test q <= 0
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group := NewKmerSetGroup(k, 3)
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result = group.QuorumAtLeast(0)
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if result.Len() != 0 {
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t.Errorf("q=0: expected 0 k-mers, got %d", result.Len())
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}
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result = group.QuorumAtLeast(-1)
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if result.Len() != 0 {
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t.Errorf("q=-1: expected 0 k-mers, got %d", result.Len())
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}
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// Test q > n
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group.Get(0).AddKmerCode(1)
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result = group.QuorumAtLeast(10)
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if result.Len() != 0 {
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t.Errorf("q>n: expected 0 k-mers, got %d", result.Len())
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}
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}
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// TestQuorumAtLeastQ1 tests q=1 (should equal Union)
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func TestQuorumAtLeastQ1(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 3)
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// Add different k-mers to each set
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group.Get(0).AddKmerCode(1)
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group.Get(0).AddKmerCode(2)
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group.Get(1).AddKmerCode(2)
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group.Get(1).AddKmerCode(3)
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group.Get(2).AddKmerCode(3)
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group.Get(2).AddKmerCode(4)
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quorum := group.QuorumAtLeast(1)
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union := group.Union()
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if quorum.Len() != union.Len() {
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t.Errorf("QuorumAtLeast(1) length %d != Union length %d", quorum.Len(), union.Len())
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}
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// Check all elements match
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for kmer := uint64(1); kmer <= 4; kmer++ {
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if quorum.Contains(kmer) != union.Contains(kmer) {
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t.Errorf("Mismatch for k-mer %d", kmer)
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}
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}
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}
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// TestQuorumAtLeastQN tests q=n (should equal Intersect)
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func TestQuorumAtLeastQN(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 3)
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// Add some common k-mers and some unique
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for i := 0; i < 3; i++ {
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group.Get(i).AddKmerCode(10) // common to all
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group.Get(i).AddKmerCode(20) // common to all
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}
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group.Get(0).AddKmerCode(1) // unique to set 0
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group.Get(1).AddKmerCode(2) // unique to set 1
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quorum := group.QuorumAtLeast(3)
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intersect := group.Intersect()
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if quorum.Len() != intersect.Len() {
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t.Errorf("QuorumAtLeast(n) length %d != Intersect length %d", quorum.Len(), intersect.Len())
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}
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if quorum.Len() != 2 {
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t.Errorf("Expected 2 common k-mers, got %d", quorum.Len())
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}
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if !quorum.Contains(10) || !quorum.Contains(20) {
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t.Error("Missing common k-mers")
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}
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if quorum.Contains(1) || quorum.Contains(2) {
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t.Error("Unique k-mers should not be in result")
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}
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}
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// TestQuorumAtLeastGeneral tests general quorum values
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func TestQuorumAtLeastGeneral(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 5)
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// Setup: k-mer i appears in i sets (for i=1..5)
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// k-mer 1: in set 0
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// k-mer 2: in sets 0,1
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// k-mer 3: in sets 0,1,2
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// k-mer 4: in sets 0,1,2,3
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// k-mer 5: in sets 0,1,2,3,4 (all)
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for kmer := uint64(1); kmer <= 5; kmer++ {
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for setIdx := 0; setIdx < int(kmer); setIdx++ {
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group.Get(setIdx).AddKmerCode(kmer)
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}
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}
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tests := []struct {
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q int
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expected map[uint64]bool
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}{
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{1, map[uint64]bool{1: true, 2: true, 3: true, 4: true, 5: true}},
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{2, map[uint64]bool{2: true, 3: true, 4: true, 5: true}},
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{3, map[uint64]bool{3: true, 4: true, 5: true}},
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{4, map[uint64]bool{4: true, 5: true}},
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{5, map[uint64]bool{5: true}},
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}
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for _, tt := range tests {
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result := group.QuorumAtLeast(tt.q)
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if result.Len() != uint64(len(tt.expected)) {
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t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
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}
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for kmer := uint64(1); kmer <= 5; kmer++ {
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shouldContain := tt.expected[kmer]
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doesContain := result.Contains(kmer)
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if shouldContain != doesContain {
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t.Errorf("q=%d, k-mer=%d: expected contains=%v, got %v", tt.q, kmer, shouldContain, doesContain)
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}
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}
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}
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}
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// TestQuorumExactlyBasic tests QuorumExactly basic functionality
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func TestQuorumExactlyBasic(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 5)
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// Setup: k-mer i appears in exactly i sets
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for kmer := uint64(1); kmer <= 5; kmer++ {
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for setIdx := 0; setIdx < int(kmer); setIdx++ {
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group.Get(setIdx).AddKmerCode(kmer)
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}
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}
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tests := []struct {
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q int
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expected []uint64
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}{
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{1, []uint64{1}},
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{2, []uint64{2}},
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{3, []uint64{3}},
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{4, []uint64{4}},
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{5, []uint64{5}},
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}
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for _, tt := range tests {
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result := group.QuorumExactly(tt.q)
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if result.Len() != uint64(len(tt.expected)) {
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t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
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}
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for _, kmer := range tt.expected {
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if !result.Contains(kmer) {
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t.Errorf("q=%d: missing k-mer %d", tt.q, kmer)
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}
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}
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}
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}
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// TestQuorumIdentity tests the mathematical identity: Exactly(q) = AtLeast(q) - AtLeast(q+1)
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func TestQuorumIdentity(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 4)
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// Add random distribution
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group.Get(0).AddKmerCode(1)
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group.Get(0).AddKmerCode(2)
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group.Get(0).AddKmerCode(3)
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group.Get(1).AddKmerCode(2)
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group.Get(1).AddKmerCode(3)
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group.Get(1).AddKmerCode(4)
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group.Get(2).AddKmerCode(3)
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group.Get(2).AddKmerCode(4)
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group.Get(3).AddKmerCode(4)
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for q := 1; q <= 4; q++ {
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exactly := group.QuorumExactly(q)
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atLeast := group.QuorumAtLeast(q)
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atLeastPlus1 := group.QuorumAtLeast(q + 1)
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// Verify: every element in exactly(q) is in atLeast(q)
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iter := exactly.Iterator()
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for iter.HasNext() {
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kmer := iter.Next()
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if !atLeast.Contains(kmer) {
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t.Errorf("q=%d: k-mer %d in Exactly but not in AtLeast", q, kmer)
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}
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if atLeastPlus1.Contains(kmer) {
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t.Errorf("q=%d: k-mer %d in Exactly but also in AtLeast(q+1)", q, kmer)
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}
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}
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}
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}
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// TestQuorumDisjointSets tests quorum on completely disjoint sets
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func TestQuorumDisjointSets(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 3)
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// Each set has unique k-mers
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group.Get(0).AddKmerCode(1)
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group.Get(1).AddKmerCode(2)
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group.Get(2).AddKmerCode(3)
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// q=1 should give all
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result := group.QuorumAtLeast(1)
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if result.Len() != 3 {
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t.Errorf("Disjoint sets q=1: expected 3, got %d", result.Len())
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}
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// q=2 should give none
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result = group.QuorumAtLeast(2)
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if result.Len() != 0 {
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t.Errorf("Disjoint sets q=2: expected 0, got %d", result.Len())
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}
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}
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// TestQuorumIdenticalSets tests quorum on identical sets
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func TestQuorumIdenticalSets(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 3)
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// All sets have same k-mers
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for i := 0; i < 3; i++ {
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group.Get(i).AddKmerCode(10)
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group.Get(i).AddKmerCode(20)
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group.Get(i).AddKmerCode(30)
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}
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// Any q <= n should give all k-mers
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for q := 1; q <= 3; q++ {
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result := group.QuorumAtLeast(q)
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if result.Len() != 3 {
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t.Errorf("Identical sets q=%d: expected 3, got %d", q, result.Len())
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}
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}
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}
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// TestQuorumLargeNumbers tests with large k-mer values
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func TestQuorumLargeNumbers(t *testing.T) {
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k := 21
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group := NewKmerSetGroup(k, 3)
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// Use large uint64 values (actual k-mer encodings)
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largeKmers := []uint64{
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0x1234567890ABCDEF,
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0xFEDCBA0987654321,
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0xAAAAAAAAAAAAAAAA,
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}
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// Add to multiple sets
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for i := 0; i < 3; i++ {
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for j := 0; j <= i; j++ {
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group.Get(j).AddKmerCode(largeKmers[i])
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}
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}
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result := group.QuorumAtLeast(2)
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if result.Len() != 2 {
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t.Errorf("Large numbers q=2: expected 2, got %d", result.Len())
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}
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if !result.Contains(largeKmers[1]) || !result.Contains(largeKmers[2]) {
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t.Error("Large numbers: wrong k-mers in result")
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}
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}
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// TestQuorumAtMostBasic tests QuorumAtMost basic functionality
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func TestQuorumAtMostBasic(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 5)
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// Setup: k-mer i appears in exactly i sets
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for kmer := uint64(1); kmer <= 5; kmer++ {
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for setIdx := 0; setIdx < int(kmer); setIdx++ {
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group.Get(setIdx).AddKmerCode(kmer)
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}
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}
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tests := []struct {
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q int
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expected []uint64
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}{
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{0, []uint64{}}, // at most 0: none
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{1, []uint64{1}}, // at most 1: only k-mer 1
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{2, []uint64{1, 2}}, // at most 2: k-mers 1,2
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{3, []uint64{1, 2, 3}}, // at most 3: k-mers 1,2,3
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{4, []uint64{1, 2, 3, 4}}, // at most 4: k-mers 1,2,3,4
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{5, []uint64{1, 2, 3, 4, 5}}, // at most 5: all k-mers
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{10, []uint64{1, 2, 3, 4, 5}}, // at most 10: all k-mers
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}
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for _, tt := range tests {
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result := group.QuorumAtMost(tt.q)
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if result.Len() != uint64(len(tt.expected)) {
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t.Errorf("q=%d: expected %d k-mers, got %d", tt.q, len(tt.expected), result.Len())
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}
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for _, kmer := range tt.expected {
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if !result.Contains(kmer) {
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t.Errorf("q=%d: missing k-mer %d", tt.q, kmer)
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}
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}
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}
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}
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// TestQuorumComplementIdentity tests that AtLeast and AtMost are complementary
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func TestQuorumComplementIdentity(t *testing.T) {
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k := 5
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group := NewKmerSetGroup(k, 4)
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// Add random distribution
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group.Get(0).AddKmerCode(1)
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group.Get(0).AddKmerCode(2)
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group.Get(0).AddKmerCode(3)
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group.Get(1).AddKmerCode(2)
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group.Get(1).AddKmerCode(3)
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group.Get(1).AddKmerCode(4)
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group.Get(2).AddKmerCode(3)
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group.Get(2).AddKmerCode(4)
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group.Get(3).AddKmerCode(4)
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union := group.Union()
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for q := 1; q < 4; q++ {
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atMost := group.QuorumAtMost(q)
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atLeast := group.QuorumAtLeast(q + 1)
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// Verify: AtMost(q) ∪ AtLeast(q+1) = Union()
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combined := atMost.Union(atLeast)
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if combined.Len() != union.Len() {
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t.Errorf("q=%d: AtMost(q) ∪ AtLeast(q+1) has %d k-mers, Union has %d",
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q, combined.Len(), union.Len())
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}
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// Verify: AtMost(q) ∩ AtLeast(q+1) = ∅
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overlap := atMost.Intersect(atLeast)
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if overlap.Len() != 0 {
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t.Errorf("q=%d: AtMost(q) and AtLeast(q+1) overlap with %d k-mers",
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q, overlap.Len())
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}
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}
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}
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// BenchmarkQuorumAtLeast benchmarks quorum operations
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func BenchmarkQuorumAtLeast(b *testing.B) {
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k := 21
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n := 10
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group := NewKmerSetGroup(k, n)
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// Populate with realistic data
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for i := 0; i < n; i++ {
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for j := uint64(0); j < 10000; j++ {
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if (j % uint64(n)) <= uint64(i) {
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group.Get(i).AddKmerCode(j)
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}
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}
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}
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b.ResetTimer()
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for i := 0; i < b.N; i++ {
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_ = group.QuorumAtLeast(5)
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}
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}
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