refactor: implement RoutableSuperKmer and update k-mer indexing pipeline

Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
2026-04-29 22:52:42 +02:00
parent 4e26e3bd40
commit 27f5e88a7b
72 changed files with 10093 additions and 1626 deletions
@@ -10,7 +10,7 @@
      
      
      
-        <link rel="next" href="theory/kmers/">
+        <link rel="next" href="kmers/">
      
      
        
@@ -297,7 +297,7 @@
  
  
    <li class="md-nav__item">
-      <a href="theory/kmers/" class="md-nav__link">
+      <a href="kmers/" class="md-nav__link">
        
  
  
@@ -380,6 +380,34 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="theory/minimizer/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Minimizer selection
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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+  
    <li class="md-nav__item">
      <a href="theory/indexing/" class="md-nav__link">
        
@@ -574,6 +602,34 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="implementation/obipipeline/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obipipeline library
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
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    <li class="md-nav__item">
      <a href="implementation/storage/" class="md-nav__link">
        
@@ -624,6 +680,34 @@

              
            
+              
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+  
+  
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+    <li class="md-nav__item">
+      <a href="implementation/unitig_evidence/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Unitig evidence encoding
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>