--- orig/SOAPdenovo-V1.05/src/63mer/bubble.c	2011-02-22 07:10:34.000000000 +0100
+++ src/bubble.c	2014-04-21 15:00:41.650723014 +0200
@@ -66,6 +66,8 @@
 static int slowSeqLength;
 
 static Time * times;
+static int * nodeCounts;
+
 static unsigned int * previous;
 static unsigned int expCounter;
 static unsigned int * expanded;
@@ -376,6 +378,8 @@
 	int Choice1, Choice2, Choice3;
 	int maxScore;
 
+	int minOverlap=overlaplen/2;
+
 	if ( length1 == 0 || length2 == 0 )
 	{
 		caseA++;
@@ -388,11 +392,13 @@
 		return 0;
 	}
 
+	/*
 	if ( length1 < overlaplen - 1 || length2 < overlaplen - 1 )
 	{
 		caseB++;
 		return 0;
 	}
+*/
 
 	/*
 	    if (length1 < overlaplen || length2 < overlaplen){
@@ -426,6 +432,16 @@
 	maxScore = Fmatrix[length1][length2];
 	maxLength = ( length1 > length2 ? length1 : length2 );
 
+	if(maxScore == maxLength)
+		return 1;
+
+	if(length1 < minOverlap || length2 < minOverlap )
+		{
+		caseB++;
+		return 0;
+		}
+
+
 	if ( maxScore < maxLength - DIFF )
 	{
 		caseC++;
@@ -1740,6 +1756,13 @@
 		fflush ( stdout );
 	}
 
+	int nodeCount=nodeCounts[origin]+1;
+
+	if(nodeCount>MAXNODELENGTH)
+		return;
+
+	nodeCounts[destination]=nodeCount;
+
 	totalTime = originTime + arcTime;
 	/*
 	if(destination==289129||destination==359610){
@@ -1843,10 +1866,48 @@
     }
 }
 */
+
+static void tourBusCleanup()
+{
+	int i;
+	ARC * parc;
+
+	for(i=0;i<expCounter;i++)
+		{
+		int node=expanded[i];
+
+		times[node] = -1;
+		previous[node] = 0;
+		dheapNodes[node] = NULL;
+
+		parc = edge_array[node].arcs;
+
+		while ( parc )
+			{
+			int target=parc->to_ed;
+
+			times[target] = -1;
+			previous[target] = 0;
+			dheapNodes[target] = NULL;
+
+			parc = parc->next;
+			}
+		}
+
+}
+
 static void tourBus ( unsigned int startingPoint )
 {
 	unsigned int currentNode = startingPoint;
+
+	unsigned int index;
+
+	if(startingPoint % 10000 == 0)
+		printf("tourBus() ************************************************************************************************** FROM %i \n",startingPoint);
+
 	times[startingPoint] = 0;
+	nodeCounts[startingPoint] = 0;
+
 	previous[startingPoint] = currentNode;
 
 	while ( currentNode > 0 )
@@ -1858,8 +1919,91 @@
 		if ( currentNode > 0 )
 			{ rnodeCounter++; }
 	}
+
+	tourBusCleanup();
 }
 
+
+void dumpEdges()
+{
+	int i;
+	ARC *parc;
+
+	for ( i = 1; i <= num_ed; i++ ) //num_ed
+	{
+		EDGE *edge=edge_array+i;
+
+		if (edge->deleted)
+			continue;
+
+		printf("Edge %i:\n",i);
+
+		if(edge->length>0)
+			printTightString(edge->seq, edge->length);
+		else
+			printf("\n");
+
+		int hasA=0, hasC=0, hasG=0, hasT=0;
+
+		parc=edge->arcs;
+		while(parc!=NULL)
+			{
+			int toEd=parc->to_ed;
+
+			EDGE *toEdge=edge_array+toEd;
+
+			if(toEdge->length>0)
+				{
+				char ch=getCharInTightString(toEdge->seq,0);
+				switch(ch)
+				{
+				case 0:
+					hasA++;
+					break;
+				case 1:
+					hasC++;
+					break;
+				case 2:
+					hasT++;
+					break;
+				case 3:
+					hasG++;
+					break;
+				}
+				}
+
+			parc=parc->next;
+			}
+
+		if(hasA>1 || hasC>1 || hasT>1 || hasG>1)
+			{
+			printf("%i %i %i %i\n", hasA, hasC, hasT, hasG);
+			}
+
+		parc=edge->arcs;
+		while(parc!=NULL)
+			{
+			int toEd=parc->to_ed;
+
+			EDGE *toEdge=edge_array+toEd;
+
+			printf("(%i) ",toEd);
+
+			if(toEdge->length>0)
+				printTightString(toEdge->seq, toEdge->length);
+			else
+				printf("\n");
+
+			parc=parc->next;
+
+			}
+
+
+		printf("\n");
+	}
+}
+
+
 void bubblePinch ( double simiCutoff, char * outfile, int M )
 {
 	unsigned int index, counter = 0;
@@ -1884,24 +2028,25 @@
 
 	if ( M <= 1 )
 	{
-		MAXNODELENGTH = 3;
+		MAXNODELENGTH = 10;
 		DIFF = 2;
 	}
 	else if ( M == 2 )
 	{
-		MAXNODELENGTH = 9;
+		MAXNODELENGTH = 20;
 		DIFF = 3;
 	}
 	else
 	{
 		MAXNODELENGTH = 30;
-		DIFF = 10;
+		DIFF = 4;
 	}
 
 	printf ( "start to pinch bubbles, cutoff %f, MAX NODE NUM %d, MAX DIFF %d\n",
 	         cutoff, MAXNODELENGTH, DIFF );
 	createRVmemo();
 	times = ( Time * ) ckalloc ( ( num_ed + 1 ) * sizeof ( Time ) );
+	nodeCounts = (int * )ckalloc ((num_ed + 1) * sizeof (int));
 	previous = ( unsigned int * ) ckalloc ( ( num_ed + 1 ) * sizeof ( unsigned int ) );
 	expanded = ( unsigned int * ) ckalloc ( ( num_ed + 1 ) * sizeof ( unsigned int ) );
 	dheapNodes = ( DFibHeapNode ** ) ckalloc ( ( num_ed + 1 ) * sizeof ( DFibHeapNode * ) );
@@ -1916,6 +2061,7 @@
 
 	dheap = newDFibHeap();
 	eligibleStartingPoints = ( unsigned int * ) ckalloc ( ( num_ed + 1 ) * sizeof ( unsigned int ) );
+
 	resetNodeStatus();
 	//determineEligibleStartingPoints();
 	createArcLookupTable();
@@ -1927,7 +2073,7 @@
 		//printf("starting point %d with length %d\n",startingNode,edge_array[startingNode].length);
 		expCounter = 0;
 		tourBus ( startingNode );
-		updateNodeStatus();
+//		updateNodeStatus();
 	}
 
 	resetNodeStatus();
@@ -1942,6 +2088,7 @@
 	free ( ( void * ) eligibleStartingPoints );
 	destroyDHeap ( dheap );
 	free ( ( void * ) dheapNodes );
+	free ( ( void * ) nodeCounts );
 	free ( ( void * ) times );
 	free ( ( void * ) previous );
 	free ( ( void * ) expanded );