docs: document k-mer index architecture and refactor distance metrics

Add comprehensive documentation for the `obilayeredmap` crate, `PersistentCompactIntVec`, `PersistentBitVec`, and the hierarchical k-mer index architecture, including sidebar navigation updates across all documentation pages. Refactor the Bray-Curtis distance computation in `obicompactvec` to decouple numerator and denominator calculations, replacing direct pairwise calls with explicit loops over precomputed sums. Update tests to verify column sum accuracy and align with the simplified API.
2026-05-15 21:07:23 +08:00
parent 8409c852ef
commit 45d49ed501
25 changed files with 8842 additions and 117 deletions
@@ -740,6 +740,90 @@

              
            
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+  
+  
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+    <li class="md-nav__item">
+      <a href="../implementation/obilayeredmap/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
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+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/persistent_compact_int_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
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+              
+            
+              
+                
+  
+  
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+    <li class="md-nav__item">
+      <a href="../implementation/persistent_bit_vec/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
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+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
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+              
+            
          </ul>
        </nav>
      
@@ -822,6 +906,34 @@

              
            
+              
+                
+  
+  
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+    <li class="md-nav__item">
+      <a href="../architecture/index_architecture/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
+  </span>
+  
+  
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+      </a>
+    </li>
+  
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+              
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          </ul>
        </nav>