tweak to simplifications

GATB · Nov 5, 2023 · 3bd86d6 · 3bd86d6
1 parent dca6577
commit 3bd86d6
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
@@ -133,6 +133,21 @@ void Simplifications<GraphType,Node,Edge>::simplify()
                 && _nbTipRemovalPasses < 20);
     }
 
+    // do one round of bubble removal, then one EC, then go on with the rest of the rounds
+    // that's because bubble removal gets much faster after EC
+
+    nbBubblesRemovedPreviously = nbBubblesRemoved;
+    nbBubblesRemoved = removeBulges();
+    if (bubbleRemoval.size() != 0)
+        bubbleRemoval += " + ";
+    bubbleRemoval += to_string(nbBubblesRemoved);
+
+    nbECRemovedPreviously = nbECRemoved;
+    nbECRemoved = removeErroneousConnections(); // now we're using bulges removal, not bubbles (to follow SPAdes)
+    if (ECRemoval.size() != 0)
+        ECRemoval += " + ";
+    ECRemoval += to_string(nbECRemoved);
+
     if (_doBulgeRemoval)
     {
         do