Add mode3::AssembyGraph::run4.

src/mode3-AssemblyGraph.hpp

@@ -389,11 +389,15 @@ class shasta::mode3::AssemblyGraph:
         bool assembleSequence,
         bool debug);
 
-    // Alternate version for testing.
+    // Alternate versions for testing.
     void run3(
         uint64_t threadCount,
         bool assembleSequence,
         bool debug);
+    void run4(
+        uint64_t threadCount,
+        bool assembleSequence,
+        bool debug);
 
 
 

src/mode3-AssemblyGraphDetangle4.cpp

@@ -0,0 +1,64 @@
+// Shasta.
+#include "mode3-AssemblyGraph.hpp"
+#include "AssemblerOptions.hpp"
+#include "performanceLog.hpp"
+#include "timestamp.hpp"
+using namespace shasta;
+using namespace mode3;
+
+
+
+void AssemblyGraph::run4(
+    uint64_t threadCount,
+    bool /* assembleSequence */,
+    bool debug)
+{
+    cout << "AssemblyGraph::run4 begins for component " << componentId << endl;
+
+    SHASTA_ASSERT(std::is_sorted(orientedReadIds.begin(), orientedReadIds.end()));
+    SHASTA_ASSERT(std::is_sorted(anchorIds.begin(), anchorIds.end()));
+
+    write("A");
+
+    compress();
+    for(uint64_t iteration=0; ; iteration ++) {
+        performanceLog << timestamp << "Iteration " << iteration <<
+            " of bubble cleanup begins." << endl;
+        const uint64_t cleanedUpBubbleCount = cleanupBubbles(
+            debug,
+            options.assemblyGraphOptions.bubbleCleanupMaxOffset,
+            options.assemblyGraphOptions.chainTerminalCommonThreshold,
+            threadCount);
+        if(cleanedUpBubbleCount == 0) {
+            break;
+        }
+        cout << "Cleaned up " << cleanedUpBubbleCount << " bubbles." << endl;
+        compressBubbleChains();
+        compress();
+    }
+
+    expand();
+    // Using the Bayesian model can sometimes generate adjacent anchor pairs without common reads.
+    const bool useBayesianModel = true;
+    write("B");
+    detangleEdges(false,
+        options.assemblyGraphOptions.detangleToleranceLow,      // Use 1
+        options.assemblyGraphOptions.detangleToleranceHigh,     // Use 3
+        useBayesianModel,
+        options.assemblyGraphOptions.epsilon,
+        options.assemblyGraphOptions.minLogP);
+    write("C");
+    while(compressSequentialEdges());
+    compressBubbleChains();
+
+    // Expand, so we can do read following on the AssemblyGraph in the http server.
+    expand();
+    write("D");
+
+    // Assemble sequence.
+    assembleAllChainsMultithreaded(
+        options.assemblyGraphOptions.chainTerminalCommonThreshold,
+        threadCount);
+    writeAssemblyDetails();
+    write("Final", true);
+}