bio-velvet_underground 0.0.1

data/ext/src/src/concatenatedPreGraph.h

@@ -0,0 +1,29 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#ifndef _CONCATENATEDPREGRAPH_H_
+#define _CONCATENATEDPREGRAPH_H_
+
+// Concatenates all pairs of nodes which form a linear structure
+void concatenatePreGraph_pg(PreGraph * preGraph);
+
+void clipTips_pg(PreGraph * preGraph);
+
+#endif

data/ext/src/src/correctedGraph.c

@@ -0,0 +1,2642 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#include <stdlib.h>
+#include <stdio.h>
+#include <time.h>
+
+#include "globals.h"
+#include "graph.h"
+#include "tightString.h"
+#include "dfibHeap.h"
+#include "fibHeap.h"
+#include "recycleBin.h"
+#include "passageMarker.h"
+#include "concatenatedGraph.h"
+#include "graphStats.h"
+#include "utility.h"
+
+#define TICKET_BLOCK_SIZE 10000
+
+static const Time INDEL = 0;
+static const Time SIM[4][4] = {
+	{1, 0, 0, 0},
+	{0, 1, 0, 0},
+	{0, 0, 1, 0},
+	{0, 0, 0, 1}
+};
+
+typedef struct tkt_st Ticket;
+
+struct tkt_st {
+	Ticket *next;
+	IDnum id_a;
+} ATTRIBUTE_PACKED;
+
+//Global variables used throughout this procedure(internal use only !)
+static int MAXREADLENGTH = 100;
+static int MAXNODELENGTH = 200;
+static double MAXDIVERGENCE = 0.2;
+static int MAXGAPS = 3;
+
+static Time *times;
+static Node **previous;
+
+static DFibHeapNode **dheapNodes;
+static DFibHeap *dheap;
+
+static TightString *fastSequence;
+static TightString *slowSequence;
+
+static Node *activeNode;
+static Node *startingNode;
+static int WORDLENGTH;
+static Graph *graph;
+static IDnum dbgCounter;
+
+static PassageMarkerI fastPath;
+static PassageMarkerI slowPath;
+
+static IDnum *eligibleStartingPoints;
+
+static double **Fmatrix;
+static Coordinate *slowToFastMapping;
+static Coordinate *fastToSlowMapping;
+
+static RecycleBin *ticketMemory;
+
+static Ticket **todoLists;
+static Ticket **todo;
+static Ticket *done;
+static boolean *progressStatus;
+
+static ShortLength *sequenceLengths;
+static Category *sequenceCategories;
+
+//End of global variables;
+
+static void setNodeTime(Node * node, Time time)
+{
+	times[getNodeID(node) + nodeCount(graph)] = time;
+}
+
+static Time getNodeTime(Node * node)
+{
+	return times[getNodeID(node) + nodeCount(graph)];
+}
+
+static void setNodePrevious(Node * previousNode, Node * node)
+{
+	previous[getNodeID(node) + nodeCount(graph)] = previousNode;
+}
+
+static Node *getNodePrevious(Node * node)
+{
+	return previous[getNodeID(node) + nodeCount(graph)];
+}
+
+static void setNodeDHeapNode(Node * node, DFibHeapNode * dheapNode)
+{
+	dheapNodes[getNodeID(node) + nodeCount(graph)] = dheapNode;
+}
+
+static DFibHeapNode *getNodeDHeapNode(Node * node)
+{
+	return dheapNodes[getNodeID(node) + nodeCount(graph)];
+}
+
+static Ticket *newTicket()
+{
+	if (ticketMemory == NULL)
+		ticketMemory =
+		    newRecycleBin(sizeof(Ticket), TICKET_BLOCK_SIZE);
+
+	return allocatePointer(ticketMemory);
+}
+
+static boolean isPreviousToNode(Node * previous, Node * target)
+{
+	Node *currentNode = target;
+	Node *previousNode = NULL;
+	Time targetTime = getNodeTime(target);
+
+	//velvetLog("Testing if %ld is previous to %ld\n", getNodeID(previous), getNodeID(target));
+
+	while (true) {
+		if (currentNode == previous)
+			return true;
+
+		if (currentNode == previousNode)
+			return false;
+
+		if (getNodeTime(currentNode) != targetTime)
+			return false;
+
+		previousNode = currentNode;
+		currentNode = getNodePrevious(currentNode);
+	}
+}
+
+static void concatenateCommonTodoLists(Node * nodeA, Node * nodeB)
+{
+	Ticket **listA = &todoLists[getNodeID(nodeA) + nodeCount(graph)];
+	Ticket **listB = &todoLists[getNodeID(nodeB) + nodeCount(graph)];
+	Ticket *head = NULL;
+	Ticket *tail = NULL;
+	Ticket *tmp;
+	IDnum idA, idB;
+	IDnum targetID = getNodeID(nodeA);
+	IDnum indexA, indexB;
+	IDnum nodes = nodeCount(graph);
+
+	//velvetLog("Merging todo list %ld into %ld\n", getNodeID(nodeB),
+	//       getNodeID(nodeA));
+
+	if (*listB == NULL)
+		return;
+
+	if (*listA == NULL) {
+		*listA = *listB;
+		*listB = NULL;
+		return;
+	}
+
+	while (*listA != NULL && *listB != NULL) {
+		idA = (*listA)->id_a;
+		idB = (*listB)->id_a;
+		indexA = idA + nodes;
+		indexB = idB + nodes;
+
+		if (previous[indexA] == nodeA) {
+			tmp = *listA;
+			*listA = (*listA)->next;
+			deallocatePointer(ticketMemory, tmp);
+			continue;
+		}
+
+		if (idB == targetID || previous[indexB] == nodeA) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+			continue;
+		}
+
+		if (idA > idB) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+		} else if (idA < idB) {
+			tmp = *listA;
+			*listA = (*listA)->next;
+		} else {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+
+			tmp = *listA;
+			*listA = (*listA)->next;
+		}
+
+		if (tail == NULL) {
+			tail = tmp;
+			head = tail;
+		} else {
+			tail->next = tmp;
+			tail = tail->next;
+		}
+	}
+
+	while (*listA != NULL) {
+		idA = (*listA)->id_a;
+		indexA = idA + nodes;
+
+		if (previous[indexA] == nodeA) {
+			tmp = *listA;
+			*listA = (*listA)->next;
+			deallocatePointer(ticketMemory, tmp);
+		} else if (tail != NULL) {
+			tail->next = *listA;
+			*listA = (*listA)->next;
+			tail = tail->next;
+		} else {
+			head = *listA;
+			*listA = (*listA)->next;
+			tail = head;
+		}
+	}
+
+	while (*listB != NULL) {
+		idB = (*listB)->id_a;
+		indexB = idB + nodes;
+
+		if (idB == targetID || previous[indexB] == nodeA) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+		} else if (tail != NULL) {
+			tail->next = *listB;
+			*listB = (*listB)->next;
+			tail = tail->next;
+		} else {
+			head = *listB;
+			*listB = (*listB)->next;
+			tail = head;
+
+		}
+	}
+
+	if (tail != NULL)
+		tail->next = NULL;
+
+	*listA = head;
+	*listB = NULL;
+}
+
+static void concatenateTodoListIntoActive(Node * nodeB)
+{
+	Ticket **listB = &todoLists[getNodeID(nodeB) + nodeCount(graph)];
+	Ticket *head = NULL;
+	Ticket *tail = NULL;
+	Ticket *tmp;
+	IDnum nodes = nodeCount(graph);
+	IDnum idA, idB;
+	IDnum activeID = getNodeID(activeNode);
+	IDnum indexB, indexA;
+
+	//velvetLog("Merging todo list %ld into active node %ld\n",
+	//       getNodeID(nodeB), getNodeID(activeNode));
+
+	if (*listB == NULL)
+		return;
+
+	if (*todo == NULL) {
+		*todo = *listB;
+		*listB = NULL;
+		return;
+	}
+
+	while (*todo != NULL && *listB != NULL) {
+		idA = (*todo)->id_a;
+		idB = (*listB)->id_a;
+		indexA = idA + nodes;
+		indexB = idB + nodes;
+
+		if (previous[indexA] == activeNode
+		    || progressStatus[indexA]) {
+			tmp = *todo;
+			*todo = (*todo)->next;
+			deallocatePointer(ticketMemory, tmp);
+			continue;
+		}
+
+		if (idB == activeID || previous[indexB] == activeNode
+		    || progressStatus[indexB]) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+			continue;
+		}
+
+		if (idA > idB) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+		} else if (idA < idB) {
+			tmp = *todo;
+			*todo = (*todo)->next;
+		} else {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+
+			tmp = *todo;
+			*todo = (*todo)->next;
+		}
+
+		if (tail == NULL) {
+			tail = tmp;
+			head = tail;
+		} else {
+			tail->next = tmp;
+			tail = tmp;
+		}
+	}
+
+	while (*todo != NULL) {
+		idA = (*todo)->id_a;
+		indexA = idA + nodes;
+
+		if (previous[indexA] == activeNode
+		    || progressStatus[indexA]) {
+			tmp = *todo;
+			*todo = (*todo)->next;
+			deallocatePointer(ticketMemory, tmp);
+		} else if (tail != NULL) {
+			tail->next = *todo;
+			*todo = (*todo)->next;
+			tail = tail->next;
+		} else {
+			head = *todo;
+			*todo = (*todo)->next;
+			tail = head;
+		}
+	}
+
+	while (*listB != NULL) {
+		idB = (*listB)->id_a;
+		indexB = idB + nodes;
+
+		if (idB == activeID || previous[indexB] == activeNode
+		    || progressStatus[indexB]) {
+			tmp = *listB;
+			*listB = (*listB)->next;
+			deallocatePointer(ticketMemory, tmp);
+		} else if (tail != NULL) {
+			tail->next = *listB;
+			*listB = (*listB)->next;
+			tail = tail->next;
+		} else {
+			head = *listB;
+			*listB = (*listB)->next;
+			tail = head;
+
+		}
+	}
+
+	if (tail != NULL)
+		tail->next = NULL;
+	*todo = head;
+	*listB = NULL;
+}
+
+static void concatenateTodoLists(Node * nodeA, Node * nodeB)
+{
+	if (nodeA == activeNode)
+		concatenateTodoListIntoActive(nodeB);
+	else
+		concatenateCommonTodoLists(nodeA, nodeB);
+}
+
+static IDnum nextTodoTicket()
+{
+	Ticket *tkt;
+	IDnum index;
+
+	while (*todo != NULL) {
+		tkt = *todo;
+		*todo = tkt->next;
+
+		index = tkt->id_a + nodeCount(graph);
+
+		if (previous[index] == activeNode) {
+			deallocatePointer(ticketMemory, tkt);
+			continue;
+		}
+
+		progressStatus[index] = true;
+
+		tkt->next = done;
+		done = tkt;
+
+		return tkt->id_a;
+	}
+
+	return 0;
+}
+
+static void freeDoneTickets()
+{
+	Ticket *tkt;
+	IDnum nodes = nodeCount(graph);
+
+	while (done != NULL) {
+		tkt = done;
+		done = tkt->next;
+		progressStatus[tkt->id_a + nodes] = false;
+		deallocatePointer(ticketMemory, tkt);
+	}
+}
+
+static void updateNodeStatus(Node * node)
+{
+	FibHeap *heap = newFibHeap();
+	Arc *arc;
+	Node *currentNode = node;
+	Node *destination;
+
+	setNodeStatus(currentNode, true);
+
+	while (currentNode != NULL) {
+		for (arc = getArc(currentNode); arc != NULL;
+		     arc = getNextArc(arc)) {
+			destination = getDestination(arc);
+			if (getNodeStatus(destination) > 1) {
+				setNodeStatus(destination, true);
+				insertNodeIntoHeap(heap,
+						   getNodeID(destination),
+						   destination);
+			}
+		}
+
+		currentNode = removeNextNodeFromHeap(heap);
+	}
+
+	destroyHeap(heap);
+}
+
+static void determineEligibleStartingPoints()
+{
+	IDnum nodeIndex;
+	IDnum maxmult;
+	Node *node;
+	Arc *arc;
+	IDnum counter = 0;
+	FibHeap *heap = newFibHeap();
+
+	velvetLog("Determining eligible starting points\n");
+
+	for (nodeIndex = 1; nodeIndex <= nodeCount(graph); nodeIndex++) {
+		node = getNodeInGraph(graph, nodeIndex);
+		if (node == NULL)
+			continue;
+
+		maxmult = 0;
+		for (arc = getArc(node); arc != NULL;
+		     arc = getNextArc(arc))
+			if (getMultiplicity(arc) > maxmult)
+				maxmult = getMultiplicity(arc);
+
+		insertNodeIntoHeap(heap, -maxmult, node);
+
+		// Same for twin node
+		node = getNodeInGraph(graph, -nodeIndex);
+		maxmult = 0;
+		for (arc = getArc(node); arc != NULL;
+		     arc = getNextArc(arc))
+			if (getMultiplicity(arc) > maxmult)
+				maxmult = getMultiplicity(arc);
+
+		insertNodeIntoHeap(heap, -maxmult, node);
+	}
+
+	while ((node = removeNextNodeFromHeap(heap)) != NULL)
+		eligibleStartingPoints[counter++] = getNodeID(node);
+
+	destroyHeap(heap);
+	velvetLog("Done listing starting nodes\n");
+}
+
+static Node *nextStartingPoint()
+{
+	static IDnum counter = 0;
+	Node *result = NULL;
+
+	while (result == NULL || getNodeStatus(result) > 0) {
+		if (counter >= nodeCount(graph) * 2)
+			return NULL;
+
+		result =
+		    getNodeInGraph(graph,
+				   eligibleStartingPoints[counter++]);
+	}
+
+	return result;
+}
+
+static boolean
+extractSequence(PassageMarkerI path, TightString * sequence)
+{
+	PassageMarkerI marker;
+	Coordinate seqLength = 0;
+	Coordinate writeIndex = 0;
+
+	//velvetLog("Extracting sequence %ld ... ", pathLength);
+
+	//Measure length
+	for (marker = getNextInSequence(path); !isTerminal(marker);
+	     marker = getNextInSequence(marker))
+		seqLength += getNodeLength(getNode(marker));
+
+	if (seqLength > MAXREADLENGTH)
+		return false;
+	else
+		setTightStringLength(sequence, seqLength);
+
+	//Copy sequences
+	for (marker = getNextInSequence(path); !isTerminal(marker);
+	     marker = getNextInSequence(marker)) {
+		appendNodeSequence(getNode(marker), sequence, writeIndex);
+		writeIndex += getNodeLength(getNode(marker));
+	}
+
+	return true;
+}
+
+static Time max(Time A, Time B, Time C)
+{
+	if (A >= B && A >= C)
+		return A;
+	else if (B >= C)
+		return B;
+	else
+		return C;
+}
+
+static boolean
+compareSequences(TightString * sequence1, TightString * sequence2)
+{
+	Coordinate i, j;
+	Coordinate length1 = getLength(sequence1);
+	Coordinate length2 = getLength(sequence2);
+	Coordinate maxLength;
+	Time Choice1, Choice2, Choice3;
+	Time maxScore;
+
+	if (length1 == 0 || length2 == 0)
+		return false;
+
+	maxLength = (length1 > length2 ? length1 : length2);
+
+	if (length1 < WORDLENGTH || length2 < WORDLENGTH) {
+		if (maxLength - length1 > MAXGAPS
+		    || maxLength - length2 > MAXGAPS)
+			return false;
+		if (WORDLENGTH - length1 > MAXGAPS
+		    || WORDLENGTH - length2 > MAXGAPS)
+			return false;
+	}
+
+	for (i = 0; i <= length1; i++)
+		Fmatrix[i][0] = 0;
+	for (j = 0; j <= length2; j++)
+		Fmatrix[0][j] = 0;
+
+	for (i = 1; i <= length1; i++) {
+		for (j = 1; j <= length2; j++) {
+			Choice1 =
+			    Fmatrix[i - 1][j - 1] +
+			    SIM[(int) getNucleotide(i - 1, sequence1)]
+			    [(int) getNucleotide(j - 1, sequence2)];
+			Choice2 = Fmatrix[i - 1][j] + INDEL;
+			Choice3 = Fmatrix[i][j - 1] + INDEL;
+			Fmatrix[i][j] = max(Choice1, Choice2, Choice3);
+		}
+	}
+
+	maxScore = Fmatrix[length1][length2];
+
+	if (maxScore < maxLength - MAXGAPS)
+		return false;
+
+	if ((1 - maxScore / maxLength) > MAXDIVERGENCE)
+		return false;
+
+	return true;
+}
+
+static void mapSlowOntoFast()
+{
+	Coordinate slowIndex = getLength(slowSequence);
+	Coordinate fastIndex = getLength(fastSequence);
+	int fastn, slown;
+
+	if (slowIndex == 0) {
+		slowToFastMapping[0] = fastIndex;
+
+		while (fastIndex >= 0)
+			fastToSlowMapping[fastIndex--] = 0;
+
+		return;
+	}
+
+	if (fastIndex == 0) {
+		while (slowIndex >= 0)
+			slowToFastMapping[slowIndex--] = 0;
+
+		fastToSlowMapping[0] = slowIndex;
+
+		return;
+	}
+
+	while (slowIndex > 0 && fastIndex > 0) {
+		fastn = (int) getNucleotide(fastIndex - 1, fastSequence);
+		slown = (int) getNucleotide(slowIndex - 1, slowSequence);
+
+		if (Fmatrix[fastIndex][slowIndex] ==
+		    Fmatrix[fastIndex - 1][slowIndex - 1] +
+		    SIM[fastn][slown]) {
+			fastToSlowMapping[--fastIndex] = --slowIndex;
+			slowToFastMapping[slowIndex] = fastIndex;
+		} else if (Fmatrix[fastIndex][slowIndex] ==
+			   Fmatrix[fastIndex - 1][slowIndex] + INDEL)
+			fastToSlowMapping[--fastIndex] = slowIndex - 1;
+
+		else if (Fmatrix[fastIndex][slowIndex] ==
+			 Fmatrix[fastIndex][slowIndex - 1] + INDEL)
+			slowToFastMapping[--slowIndex] = fastIndex - 1;
+
+		else {
+			velvetLog("Error\n");
+			fflush(stdout);
+			abort();
+		}
+	}
+
+	while (slowIndex > 0)
+		slowToFastMapping[--slowIndex] = -1;
+	while (fastIndex > 0)
+		fastToSlowMapping[--fastIndex] = -1;
+
+	slowToFastMapping[getLength(slowSequence)] =
+	    getLength(fastSequence);
+	fastToSlowMapping[getLength(fastSequence)] =
+	    getLength(slowSequence);
+}
+
+static void remapNodeArcsOntoTarget(Node * source, Node * target)
+{
+	Arc *arc;
+
+	if (source == activeNode) {
+		activeNode = target;
+		todo =
+		    &todoLists[getNodeID(activeNode) + nodeCount(graph)];
+	}
+	concatenateTodoLists(target, source);
+
+	arc = getArc(source);
+	while (arc != NULL) {
+		createAnalogousArc(target, getDestination(arc), arc, graph);
+		destroyArc(arc, graph);
+		arc = getArc(source);
+	}
+}
+
+static void remapNodeArcsOntoNeighbour(Node * source, Node * target)
+{
+	remapNodeArcsOntoTarget(source, target);
+	remapNodeArcsOntoTarget(getTwinNode(source), getTwinNode(target));
+}
+
+static void remapNodeMarkersOntoNeighbour(Node * source,
+					  PassageMarkerI sourceMarker,
+					  Node * target,
+					  PassageMarkerI targetMarker)
+{
+	PassageMarkerI marker;
+	Coordinate offset;
+	IDnum sourceLength, index;
+	ShortReadMarker *sourceArray, *shortMarker;
+	Coordinate position;
+
+	Coordinate targetStart = getPassageMarkerStart(targetMarker);
+	Coordinate targetFinish = getPassageMarkerFinish(targetMarker);
+	Coordinate sourceStart = getPassageMarkerStart(sourceMarker);
+	Coordinate sourceFinish = getPassageMarkerFinish(sourceMarker);
+
+	Coordinate alignedTargetLength = targetFinish - targetStart;
+	Coordinate alignedSourceLength = sourceFinish - sourceStart;
+
+	Coordinate realTargetLength = getNodeLength(target);
+	Coordinate realSourceLength = getNodeLength(source);
+
+	while (getMarker(source) != NULL_IDX) {
+		marker = getMarker(source);
+		extractPassageMarker(marker);
+		transposePassageMarker(marker, target);
+
+		if (realSourceLength != 0 && alignedTargetLength != 0) {
+			if (isInitial(marker)) {
+				offset = getStartOffset(marker);
+				offset *= alignedSourceLength;
+				offset /= realSourceLength;
+				offset += sourceStart;
+				offset = slowToFastMapping[offset];
+				offset -= targetStart;
+				offset *= realTargetLength;
+				offset /= alignedTargetLength;
+
+				if (offset < 0)
+					offset = 0;
+				if (offset > realTargetLength)
+					offset = realTargetLength;
+			} else
+				offset = 0;
+
+			setStartOffset(marker, offset);
+
+			if (isTerminal(marker)) {
+				offset = getFinishOffset(marker);
+				offset *= alignedSourceLength;
+				offset /= realSourceLength;
+				offset = sourceFinish - offset;
+				offset = slowToFastMapping[offset];
+				offset = targetFinish - offset;
+				offset *= realTargetLength;
+				offset /= alignedTargetLength;
+
+				if (offset < 0)
+					offset = 0;
+				if (offset > realTargetLength)
+					offset = realTargetLength;
+			} else
+				offset = 0;
+
+			setFinishOffset(marker, offset);
+		} else {
+			setStartOffset(marker, 0);
+			setFinishOffset(marker, 0);
+		}
+	}
+
+	// Short read markers 
+	if (readStartsAreActivated(graph)) {
+		// Update Coordinates
+		sourceArray = getNodeReads(source, graph);
+		sourceLength = getNodeReadCount(source, graph);
+
+		for (index = 0; index < sourceLength; index++) {
+			shortMarker =
+			    getShortReadMarkerAtIndex(sourceArray, index);
+			position = getShortReadMarkerPosition(shortMarker);
+
+			if (position > -1) {
+				if (realSourceLength > 0
+				    && alignedTargetLength > 0) {
+					position *= alignedSourceLength;
+					position /= realSourceLength;
+					position += sourceStart;
+					position =
+					    slowToFastMapping[position];
+					position -= targetStart;
+					position *= realTargetLength;
+					position /= alignedTargetLength;
+
+					if (position < 0)
+						position = 0;
+					if (position > realTargetLength)
+						position =
+						    realTargetLength;
+				} else
+					position = 0;
+			}
+
+			setShortReadMarkerPosition(shortMarker, position);
+		}
+		mergeNodeReads(target, source, graph);
+
+		// Same but for symmetrical reads
+		sourceArray = getNodeReads(getTwinNode(source), graph);
+		sourceLength =
+		    getNodeReadCount(getTwinNode(source), graph);
+
+		for (index = 0; index < sourceLength; index++) {
+			shortMarker =
+			    getShortReadMarkerAtIndex(sourceArray, index);
+			position = getShortReadMarkerPosition(shortMarker);
+
+			if (position > -1) {
+				if (realSourceLength > 0
+				    && alignedTargetLength > 0) {
+					position =
+					    realSourceLength - position;
+					position *= alignedSourceLength;
+					position /= realSourceLength;
+					position += sourceStart;
+					position =
+					    slowToFastMapping[position];
+					position -= targetStart;
+					position *= realTargetLength;
+					position /= alignedTargetLength;
+					position =
+					    realTargetLength - position;
+
+					if (position < 0)
+						position = 0;
+					if (position > realTargetLength)
+						position =
+						    realTargetLength;
+				} else
+					position = 0;
+			}
+
+			setShortReadMarkerPosition(shortMarker, position);
+		}
+		mergeNodeReads(getTwinNode(target), getTwinNode(source),
+			       graph);
+	}
+	// Virtual reads
+#ifndef SINGLE_COV_CAT
+	Category cat;
+	for (cat = 0; cat < CATEGORIES; cat++)
+		incrementVirtualCoverage(target, cat,
+					 getVirtualCoverage(source, cat));
+#else
+	incrementVirtualCoverage(target, getVirtualCoverage(source));
+#endif
+}
+
+static void remapBackOfNodeArcsOntoNeighbour(Node * source, Node * target)
+{
+	Arc *arc;
+
+	remapNodeArcsOntoTarget(getTwinNode(source), getTwinNode(target));
+	for (arc = getArc(source); arc != NULL; arc = getNextArc(arc))
+		createAnalogousArc(target, source, arc, graph);
+
+}
+
+static Coordinate
+remapBackOfNodeMarkersOntoNeighbour(Node * source,
+				    PassageMarkerI sourceMarker,
+				    Node * target,
+				    PassageMarkerI targetMarker,
+				    boolean slowToFast)
+{
+	PassageMarkerI marker, newMarker, previousMarker, nextMarker;
+	Coordinate halfwayPoint, halfwayPointOffset, breakpoint,
+	    newStartOffset, newFinishOffset;
+	Coordinate *targetToSourceMapping, *sourceToTargetMapping;
+	ShortReadMarker *selectedShortReads, *shortRead;
+	IDnum selectedShortReadCount, shortReadIndex;
+	Coordinate position;
+
+	Coordinate targetStart = getPassageMarkerStart(targetMarker);
+	Coordinate targetFinish = getPassageMarkerFinish(targetMarker);
+	Coordinate sourceStart = getPassageMarkerStart(sourceMarker);
+	Coordinate sourceFinish = getPassageMarkerFinish(sourceMarker);
+
+	Coordinate alignedTargetLength = targetFinish - targetStart;
+	Coordinate alignedSourceLength = sourceFinish - sourceStart;
+
+	Coordinate realTargetLength = getNodeLength(target);
+	Coordinate realSourceLength = getNodeLength(source);
+
+	if (slowToFast) {
+		sourceToTargetMapping = slowToFastMapping;
+		targetToSourceMapping = fastToSlowMapping;
+	} else {
+		sourceToTargetMapping = fastToSlowMapping;
+		targetToSourceMapping = slowToFastMapping;
+	}
+
+	// Calculating source node breakpoint:
+	if (alignedSourceLength > 0 && targetFinish > 0) {
+		halfwayPoint =
+		    targetToSourceMapping[targetFinish - 1] - sourceStart +
+		    1;
+		halfwayPoint *= realSourceLength;
+		halfwayPoint /= alignedSourceLength;
+	} else
+		halfwayPoint = 0;
+
+	if (halfwayPoint < 0)
+		halfwayPoint = 0;
+	if (halfwayPoint > realSourceLength)
+		halfwayPoint = realSourceLength;
+	halfwayPointOffset = realSourceLength - halfwayPoint;
+
+	// Complete markers
+	for (marker = getMarker(source); marker != NULL_IDX;
+	     marker = nextMarker) {
+		nextMarker = getNextInNode(marker);
+
+		// To avoid making loops...
+		if (getNode(getPreviousInSequence(marker)) == target)
+			continue;
+
+		// Markers which are downstream of the breakpoint
+		if (getStartOffset(marker) > halfwayPoint) {
+			newStartOffset =
+			    getStartOffset(marker) - halfwayPoint;
+			setStartOffset(marker, newStartOffset);
+			continue;
+		}
+		// Markers which are upstream of the breakpoint
+		if (getFinishOffset(marker) > halfwayPointOffset) {
+			if (slowToFast) {
+				if (realSourceLength > 0
+				    && alignedTargetLength > 0) {
+					newFinishOffset =
+					    getFinishOffset(marker) -
+					    halfwayPointOffset;
+					newFinishOffset *=
+					    alignedSourceLength;
+					newFinishOffset /=
+					    realSourceLength;
+					newFinishOffset *=
+					    realTargetLength;
+					newFinishOffset /=
+					    alignedTargetLength;
+					if (newFinishOffset < 0)
+						newFinishOffset = 0;
+					else if (newFinishOffset >
+						 realTargetLength)
+						newFinishOffset =
+						    realTargetLength;
+				} else
+					newFinishOffset = 0;
+			} else {
+				newFinishOffset =
+				    getFinishOffset(marker) -
+				    halfwayPointOffset;
+			}
+			setFinishOffset(marker, newFinishOffset);
+			extractPassageMarker(marker);
+			transposePassageMarker(marker, target);
+			continue;
+		}
+		// Markers on both sides of the divide
+		newMarker =
+		    addPassageMarker(getPassageMarkerSequenceID(marker),
+				     getPassageMarkerStart(marker),
+				     target);
+
+		setPassageMarkerStart(newMarker,
+				      getPassageMarkerStart(marker));
+		setPassageMarkerStatus(newMarker,
+				       getPassageMarkerStatus(marker));
+
+		if (realSourceLength - getStartOffset(marker) -
+		    getFinishOffset(marker) > 0) {
+			breakpoint = halfwayPoint - getStartOffset(marker);
+			breakpoint *= getPassageMarkerLength(marker);
+			breakpoint /= realSourceLength -
+			    getStartOffset(marker) -
+			    getFinishOffset(marker);
+			if (breakpoint > getPassageMarkerLength(marker))
+				breakpoint = getPassageMarkerLength(marker);
+			breakpoint *= passageMarkerDirection(marker);
+			breakpoint += getPassageMarkerStart(marker);
+		} else {
+			breakpoint = getPassageMarkerStart(marker);
+		}
+
+		setPassageMarkerFinish(newMarker, breakpoint);
+		setPassageMarkerStart(marker, breakpoint);
+
+		if (slowToFast) {
+			if (realSourceLength != 0
+			    && alignedTargetLength != 0) {
+				newStartOffset = getStartOffset(marker);
+				newStartOffset *= alignedSourceLength;
+				newStartOffset /= realSourceLength;
+				newStartOffset *= realTargetLength;
+				newStartOffset /= alignedTargetLength;
+				if (newStartOffset < 0)
+					newStartOffset = 0;
+				else if (newStartOffset > realTargetLength)
+					newStartOffset = realTargetLength;
+			} else {
+				newStartOffset = 0;
+			}
+		} else {
+			newStartOffset = getStartOffset(marker);
+		}
+
+		setStartOffset(newMarker, newStartOffset);
+		setFinishOffset(newMarker, 0);
+		setStartOffset(marker, 0);
+
+		previousMarker = getPreviousInSequence(marker);
+		setNextInSequence(previousMarker, newMarker);
+		setPreviousInSequence(previousMarker, newMarker);
+
+		setPreviousInSequence(newMarker, marker);
+		setNextInSequence(newMarker, marker);
+	}
+
+	// Read starts
+	if (readStartsAreActivated(graph)) {
+		selectedShortReads =
+		    extractBackOfNodeReads(source, halfwayPoint, graph,
+					   &selectedShortReadCount,
+					   sourceMarker, sequenceLengths);
+		if (slowToFast) {
+			if (realSourceLength > 0
+			    && alignedTargetLength > 0) {
+				for (shortReadIndex = 0;
+				     shortReadIndex <
+				     selectedShortReadCount;
+				     shortReadIndex++) {
+					shortRead =
+					    getShortReadMarkerAtIndex
+					    (selectedShortReads,
+					     shortReadIndex);
+					position =
+					    getShortReadMarkerPosition
+					    (shortRead);
+					if (position > -1) {
+						position *=
+						    alignedSourceLength;
+						position /=
+						    realSourceLength;
+						position += sourceStart;
+						position =
+						    sourceToTargetMapping
+						    [position];
+						position -= targetStart;
+						position *=
+						    realTargetLength;
+						position /=
+						    alignedTargetLength;
+						if (position < 0)
+							position = 0;
+						if (position >
+						    realTargetLength)
+							position =
+							    realTargetLength;
+					}
+					setShortReadMarkerPosition
+					    (shortRead, position);
+				}
+			} else {
+				for (shortReadIndex = 0;
+				     shortReadIndex <
+				     selectedShortReadCount;
+				     shortReadIndex++) {
+					shortRead =
+					    getShortReadMarkerAtIndex
+					    (selectedShortReads,
+					     shortReadIndex);
+					position =
+					    getShortReadMarkerPosition
+					    (shortRead);
+					if (position > -1)
+						setShortReadMarkerPosition
+						    (shortRead, 0);
+				}
+
+			}
+		}
+		injectShortReads(selectedShortReads,
+				 selectedShortReadCount, target, graph);
+
+		selectedShortReads =
+		    extractFrontOfNodeReads(getTwinNode(source),
+					    halfwayPoint, graph,
+					    &selectedShortReadCount,
+					    sourceMarker, sequenceLengths);
+		if (slowToFast) {
+			if (realSourceLength > 0
+			    && alignedTargetLength > 0) {
+				for (shortReadIndex = 0;
+				     shortReadIndex <
+				     selectedShortReadCount;
+				     shortReadIndex++) {
+					shortRead =
+					    getShortReadMarkerAtIndex
+					    (selectedShortReads,
+					     shortReadIndex);
+					position =
+					    getShortReadMarkerPosition
+					    (shortRead);
+					if (position > -1) {
+						position =
+						    getShortReadMarkerPosition
+						    (shortRead);
+						position =
+						    realSourceLength -
+						    position;
+						position *=
+						    alignedSourceLength;
+						position /=
+						    realSourceLength;
+						position += sourceStart;
+						position =
+						    sourceToTargetMapping
+						    [position];
+						position -= targetStart;
+						position *=
+						    realTargetLength;
+						position /=
+						    alignedTargetLength;
+						position =
+						    realTargetLength -
+						    position;
+						if (position < 0)
+							position = 0;
+						if (position >
+						    realTargetLength)
+							position =
+							    realTargetLength;
+					}
+					setShortReadMarkerPosition
+					    (shortRead, position);
+				}
+			} else {
+				for (shortReadIndex = 0;
+				     shortReadIndex <
+				     selectedShortReadCount;
+				     shortReadIndex++) {
+					shortRead =
+					    getShortReadMarkerAtIndex
+					    (selectedShortReads,
+					     shortReadIndex);
+					position =
+					    getShortReadMarkerPosition
+					    (shortRead);
+					if (position > -1)
+						setShortReadMarkerPosition
+						    (shortRead, 0);
+				}
+
+			}
+		}
+		injectShortReads(selectedShortReads,
+				 selectedShortReadCount,
+				 getTwinNode(target), graph);
+	}
+	// Virtual coverage
+	if (alignedSourceLength != 0) {
+		Coordinate coverage;
+#ifndef SINGLE_COV_CAT
+		Category cat;
+		for (cat = 0; cat < CATEGORIES; cat++) {
+			coverage = getVirtualCoverage(source, cat);
+			coverage *= halfwayPoint;
+			coverage /= alignedSourceLength;
+			incrementVirtualCoverage(target, cat, coverage);
+			incrementVirtualCoverage(source, cat, -coverage);
+
+			coverage = getOriginalVirtualCoverage(source, cat);
+			coverage *= halfwayPoint;
+			coverage /= alignedSourceLength;
+			incrementOriginalVirtualCoverage(source, cat,
+							 -coverage);
+		}
+#else
+		coverage = getVirtualCoverage(source);
+		coverage *= halfwayPoint;
+		coverage /= alignedSourceLength;
+		incrementVirtualCoverage(target, coverage);
+		incrementVirtualCoverage(source, -coverage);
+#endif
+	}
+
+	return halfwayPointOffset;
+}
+
+static void remapNodeInwardReferencesOntoNode(Node * source, Node * target)
+{
+	Arc *arc;
+	Node *destination;
+
+	for (arc = getArc(source); arc != NULL; arc = getNextArc(arc)) {
+		destination = getDestination(arc);
+		if (destination == target || destination == source)
+			continue;
+		if (getNodePrevious(destination) == source)
+			setNodePrevious(target, destination);
+	}
+}
+
+static void remapNodeTimesOntoTargetNode(Node * source, Node * target)
+{
+	Time nodeTime = getNodeTime(source);
+	Node *previous = getNodePrevious(source);
+	Time targetTime = getNodeTime(target);
+
+	if (nodeTime == -1)
+		return;
+
+	if (previous == source) {
+		setNodeTime(target, nodeTime);
+		setNodePrevious(target, target);
+	} else if (targetTime == -1
+		   || targetTime > nodeTime
+		   || (targetTime == nodeTime
+		       && !isPreviousToNode(target, previous))) {
+		setNodeTime(target, nodeTime);
+		if (previous != getTwinNode(source))
+			setNodePrevious(previous, target);
+		else
+			setNodePrevious(getTwinNode(target), target);
+	}
+
+	remapNodeInwardReferencesOntoNode(source, target);
+
+	setNodePrevious(NULL, source);
+}
+
+static void foldSymmetricalNode(Node * node)
+{
+	Node *twinNode = getTwinNode(node);
+	Node *tmp, *destination;
+	Arc *arc;
+	PassageMarkerI oldMarker = getMarker(node);
+	PassageMarkerI currentMarker, newMarker, previousMarker;
+	Coordinate halfwayPoint;
+	IDnum totalMult;
+
+	// Reduce time complexity of damn thing
+	if (simpleArcCount(node) < simpleArcCount(twinNode)) {
+		tmp = twinNode;
+		twinNode = node;
+		node = tmp;
+	}
+	// Destroy link to old markers 
+	setMarker(node, NULL_IDX);
+
+	// Reinsert markers properly
+	while (oldMarker != NULL_IDX) {
+		currentMarker = oldMarker;
+		oldMarker = getNextInNode(currentMarker);
+		previousMarker = getPreviousInSequence(currentMarker);
+
+		if (getNode(previousMarker) != twinNode) {
+			newMarker =
+			    addUncertainPassageMarker
+			    (getPassageMarkerSequenceID(currentMarker),
+			     twinNode);
+			setPassageMarkerStatus(newMarker,
+					       getPassageMarkerStatus
+					       (currentMarker));
+
+			setPassageMarkerStart(newMarker,
+					      getPassageMarkerStart
+					      (currentMarker));
+
+			// For security issues:
+			if (currentMarker == slowPath)
+				slowPath = newMarker;
+			else if (currentMarker == fastPath)
+				fastPath = newMarker;
+
+			halfwayPoint =
+			    (getPassageMarkerStart(currentMarker) +
+			     getPassageMarkerFinish(currentMarker))
+			    / 2;
+			setPassageMarkerFinish(newMarker, halfwayPoint);
+
+			setPassageMarkerStart(currentMarker, halfwayPoint);
+
+			setStartOffset(newMarker,
+				       getStartOffset(currentMarker));
+			setFinishOffset(newMarker, 0);
+			setStartOffset(currentMarker, 0);
+
+			setPreviousInSequence(previousMarker, newMarker);
+			setNextInSequence(previousMarker, newMarker);
+
+			setPreviousInSequence(newMarker, currentMarker);
+			setNextInSequence(newMarker, currentMarker);
+		}
+
+		transposePassageMarker(currentMarker, node);
+	}
+
+	// Read start info
+	foldSymmetricalNodeReads(node, graph);
+
+	// Coverage => already balanced!
+
+	// References
+	if (getNodeTime(node) == -1 && getNodeTime(twinNode) == -1);
+	else if (getNodeTime(node) == -1) {
+		setNodeTime(node, getNodeTime(twinNode));
+	} else if (getNodeTime(twinNode) == -1) {
+		setNodeTime(twinNode, getNodeTime(node));
+		setNodePrevious(getNodePrevious(node), twinNode);
+	} else if (getNodePrevious(node) == node) {
+		setNodeTime(twinNode, getNodeTime(node));
+		setNodePrevious(twinNode, twinNode);
+	} else if (getNodeTime(node) < getNodeTime(twinNode)) {
+		setNodeTime(twinNode, getNodeTime(node));
+		setNodePrevious(getNodePrevious(node), twinNode);
+	} else if (getNodeTime(node) == getNodeTime(twinNode)
+		   && isPreviousToNode(node, twinNode)) {
+		setNodePrevious(getNodePrevious(node), twinNode);
+	} else {
+		setNodeTime(node, getNodeTime(twinNode));
+	}
+
+	setNodePrevious(twinNode, node);
+	remapNodeInwardReferencesOntoNode(twinNode, node);
+
+	// Active node
+	if (twinNode == activeNode) {
+		activeNode = node;
+		todo =
+		    &todoLists[getNodeID(activeNode) + nodeCount(graph)];
+	}
+	concatenateTodoLists(node, twinNode);
+
+	// Remap arcs properly
+	arc = getArc(twinNode);
+	totalMult = 0;
+	while (arc != NULL) {
+		destination = getDestination(arc);
+		if (destination != node)
+			createAnalogousArc(node, destination, arc, graph);
+		totalMult += getMultiplicity(arc);
+		destroyArc(arc, graph);
+		arc = getArc(twinNode);
+	}
+
+	arc = createArc(twinNode, node, graph);
+	setMultiplicity(arc, totalMult);
+
+	// Uniqueness
+	setUniqueness(node, false);
+
+	// Starting node
+	if (startingNode == node)
+		startingNode = twinNode;
+}
+
+static void remapNodeTimesOntoNeighbour(Node * source, Node * target)
+{
+	remapNodeTimesOntoTargetNode(source, target);
+	remapNodeTimesOntoTargetNode(getTwinNode(source),
+				     getTwinNode(target));
+}
+
+static void remapNodeTimesOntoForwardMiddlePath(Node * source,
+						PassageMarkerI path)
+{
+	PassageMarkerI marker;
+	Node *target;
+	Time nodeTime = getNodeTime(source);
+	Node *previousNode = getNodePrevious(source);
+	Time targetTime;
+
+	//velvetLog("Remapping times from %ld to %ld\n", getNodeID(previousNode), getNodeID(source));
+
+	for (marker = path; getNode(marker) != source;
+	     marker = getNextInSequence(marker)) {
+		target = getNode(marker);
+		targetTime = getNodeTime(target);
+
+		//velvetLog("Through %ld\n", getNodeID(target));
+
+		if (targetTime == -1
+		    || targetTime > nodeTime
+		    || (targetTime == nodeTime
+			&& !isPreviousToNode(target, previousNode))) {
+			setNodeTime(target, nodeTime);
+			setNodePrevious(previousNode, target);
+		}
+
+		previousNode = target;
+	}
+
+	setNodePrevious(previousNode, source);
+
+}
+
+static void remapNodeTimesOntoTwinMiddlePath(Node * source,
+					     PassageMarkerI path)
+{
+	PassageMarkerI marker;
+	Node *target;
+	Node *previousNode = getTwinNode(source);
+	Time targetTime;
+	PassageMarkerI limit = getTwinMarker(getPreviousInSequence(path));
+	Time nodeTime = getNodeTime(getNode(limit));
+
+	//velvetLog("Remapping times from twins %ld to %ld\n", getNodeID(previousNode), getNodeID(getNode(limit)));
+
+	// Revving up
+	marker = path;
+	while (getNode(marker) != source)
+		marker = getNextInSequence(marker);
+	marker = getTwinMarker(marker);
+
+	// Going down the path
+	while (marker != limit) {
+		marker = getNextInSequence(marker);
+		target = getNode(marker);
+		targetTime = getNodeTime(target);
+
+		//velvetLog("Through %ld\n", getNodeID(target));
+
+		if (targetTime == -1
+		    || targetTime > nodeTime
+		    || (targetTime == nodeTime
+			&& !isPreviousToNode(target, previousNode))) {
+			setNodeTime(target, nodeTime);
+			getNodeTime(target);
+			setNodePrevious(previousNode, target);
+		}
+
+		previousNode = target;
+	}
+}
+
+static void
+remapNodeFibHeapReferencesOntoNode(Node * source, Node * target)
+{
+	DFibHeapNode *sourceDHeapNode = getNodeDHeapNode(source);
+	DFibHeapNode *targetDHeapNode = getNodeDHeapNode(target);
+
+	if (sourceDHeapNode == NULL)
+		return;
+
+	if (targetDHeapNode == NULL) {
+		setNodeDHeapNode(target, sourceDHeapNode);
+		replaceValueInDHeap(sourceDHeapNode, target);
+	} else if (getKey(targetDHeapNode) > getKey(sourceDHeapNode)) {
+		setNodeDHeapNode(target, sourceDHeapNode);
+		replaceValueInDHeap(sourceDHeapNode, target);
+		destroyNodeInDHeap(targetDHeapNode, dheap);
+	} else
+		destroyNodeInDHeap(sourceDHeapNode, dheap);
+
+	setNodeDHeapNode(source, NULL);
+}
+
+static void remapNodeOntoNeighbour(Node * source,
+				   PassageMarkerI sourceMarker,
+				   Node * target,
+				   PassageMarkerI targetMarker)
+{
+	//velvetLog("Remapping node %ld onto middle path %ld\n", getNodeID(source), getNodeID(target));
+	remapNodeMarkersOntoNeighbour(source, sourceMarker, target,
+				      targetMarker);
+
+	remapNodeTimesOntoNeighbour(source, target);
+	remapNodeArcsOntoNeighbour(source, target);
+
+	remapNodeFibHeapReferencesOntoNode(getTwinNode(source),
+					   getTwinNode(target));
+	remapNodeFibHeapReferencesOntoNode(source, target);
+
+	if (startingNode == source)
+		startingNode = target;
+	if (startingNode == getTwinNode(source))
+		startingNode = getTwinNode(target);
+
+	destroyNode(source, graph);
+}
+
+static void remapBackOfNodeDescriptorOntoNeighbour(Node * source,
+						   PassageMarkerI sourceMarker,
+						   Node * target,
+						   PassageMarkerI targetMarker,
+						   boolean slowToFast,
+						   Coordinate offset)
+{
+	//velvetLog("Splitting node descriptor %ld // %ld\n", getNodeLength(source), offset);
+
+	if (slowToFast)
+		splitNodeDescriptor(source, NULL, offset);
+	else
+		splitNodeDescriptor(source, target, offset);
+}
+
+static void remapBackOfNodeTimesOntoNeighbour(Node * source, Node * target)
+{
+	Time targetTime = getNodeTime(target);
+	Time nodeTime = getNodeTime(source);
+	Node *twinTarget = getTwinNode(target);
+	Node *twinSource = getTwinNode(source);
+	Node *previous;
+
+	if (nodeTime != -1) {
+		previous = getNodePrevious(source);
+
+		if (previous == source) {
+			setNodeTime(target, nodeTime);
+			setNodePrevious(target, target);
+		} else if (targetTime == -1
+			   || targetTime > nodeTime
+			   || (targetTime == nodeTime
+			       && !isPreviousToNode(target, previous))) {
+			setNodeTime(target, nodeTime);
+			if (previous != getTwinNode(source))
+				setNodePrevious(previous, target);
+			else
+				setNodePrevious(getTwinNode(target),
+						target);
+		}
+
+		setNodePrevious(target, source);
+	}
+
+	targetTime = getNodeTime(twinTarget);
+	nodeTime = getNodeTime(twinSource);
+
+	if (nodeTime != -1) {
+		if (targetTime == -1
+		    || targetTime > nodeTime
+		    || (targetTime == nodeTime
+			&& !isPreviousToNode(twinTarget, twinSource))) {
+			setNodeTime(twinTarget, nodeTime);
+			setNodePrevious(twinSource, twinTarget);
+		}
+	}
+
+	remapNodeInwardReferencesOntoNode(twinSource, twinTarget);
+}
+
+static void
+remapBackOfNodeOntoNeighbour(Node * source, PassageMarkerI sourceMarker,
+			     Node * target, PassageMarkerI targetMarker,
+			     boolean slowToFast)
+{
+	Coordinate offset;
+	//velvetLog("Remapping node %ld onto middle path\n", getNodeID(node));
+
+	offset =
+	    remapBackOfNodeMarkersOntoNeighbour(source, sourceMarker,
+						target, targetMarker,
+						slowToFast);
+	remapBackOfNodeDescriptorOntoNeighbour(source, sourceMarker,
+					       target, targetMarker,
+					       slowToFast, offset);
+	remapBackOfNodeTimesOntoNeighbour(source, target);
+	remapBackOfNodeArcsOntoNeighbour(source, target);
+
+	remapNodeFibHeapReferencesOntoNode(getTwinNode(source),
+					   getTwinNode(target));
+
+	if (getTwinNode(source) == startingNode)
+		startingNode = getTwinNode(target);
+}
+
+static void remapEmptyPathArcsOntoMiddlePathSimple(PassageMarkerI emptyPath,
+						   PassageMarkerI targetPath)
+{
+	PassageMarkerI pathMarker;
+	Node *start = getNode(getPreviousInSequence(emptyPath));
+	Node *finish = getNode(emptyPath);
+	Node *previousNode = start;
+	Node *currentNode;
+	Arc *originalArc = getArcBetweenNodes(start, finish, graph);
+
+	for (pathMarker = targetPath; getNode(pathMarker) != finish;
+	     pathMarker = getNextInSequence(pathMarker)) {
+		currentNode = getNode(pathMarker);
+		createAnalogousArc(previousNode, currentNode, originalArc, graph);
+		previousNode = currentNode;
+	}
+
+	createAnalogousArc(previousNode, finish, originalArc, graph);
+
+	destroyArc(originalArc, graph);
+}
+
+static void remapEmptyPathMarkersOntoMiddlePathSimple(PassageMarkerI emptyPath,
+						      PassageMarkerI targetPath)
+{
+	PassageMarkerI marker, newMarker, previousMarker, pathMarker;
+	Node *start = getNode(getPreviousInSequence(emptyPath));
+	Node *finish = getNode(emptyPath);
+	PassageMarkerI oldMarker = getMarker(finish);
+	Coordinate markerStart;
+	IDnum intersectionLength, twinIntersectionLength;
+	ShortReadMarker *intersectionReads =
+	    commonNodeReads(start, finish, graph, &intersectionLength);
+	ShortReadMarker *twinIntersectionReads =
+	    commonNodeReads(getTwinNode(start), getTwinNode(finish), graph,
+			    &twinIntersectionLength);
+
+	//velvetLog("SIMPLE %ld\t%ld\t%i\t%i\n", markerCount(finish),
+	//       getNodeID(finish), arcCount(finish),
+	//       arcCount(getTwinNode(finish)));
+
+	// Destroy link to old nodes
+	setMarker(finish, NULL_IDX);
+
+	while (oldMarker != NULL_IDX) {
+		marker = oldMarker;
+		oldMarker = getNextInNode(marker);
+		newMarker = getPreviousInSequence(marker);
+
+		if (getNode(newMarker) != start) {
+			transposePassageMarker(marker, finish);
+			continue;
+		}
+
+		markerStart = getPassageMarkerStart(marker);
+		for (pathMarker = targetPath;
+		     getNode(pathMarker) != finish;
+		     pathMarker = getNextInSequence(pathMarker)) {
+			previousMarker = newMarker;
+
+			newMarker =
+			    addUncertainPassageMarker
+			    (getPassageMarkerSequenceID(marker),
+			     getNode(pathMarker));
+			setPassageMarkerStatus(newMarker,
+					       getPassageMarkerStatus
+					       (marker));
+			setPassageMarkerStart(newMarker, markerStart);
+			setPassageMarkerFinish(newMarker, markerStart);
+			setNextInSequence(previousMarker, newMarker);
+			setPreviousInSequence(previousMarker, newMarker);
+
+			setStartOffset(newMarker, 0);
+			setFinishOffset(newMarker, 0);
+
+		}
+
+		setNextInSequence(newMarker, marker);
+		setPreviousInSequence(newMarker, marker);
+		transposePassageMarker(marker, finish);
+	}
+
+	if (readStartsAreActivated(graph)) {
+		for (pathMarker = targetPath;
+		     getNode(pathMarker) != finish;
+		     pathMarker = getNextInSequence(pathMarker)) {
+			// Read starts
+			spreadReadIDs(intersectionReads,
+				      intersectionLength,
+				      getNode(pathMarker), graph);
+			spreadReadIDs(twinIntersectionReads,
+				      twinIntersectionLength,
+				      getTwinNode(getNode(pathMarker)),
+				      graph);
+		}
+	}
+
+	free(intersectionReads);
+	free(twinIntersectionReads);
+}
+
+static boolean markerFollowsPath(PassageMarkerI marker,
+				 PassageMarkerI start,
+				 PassageMarkerI finish, Node * stopNode)
+{
+	PassageMarkerI current, path;
+
+	path = start;
+	current = marker;
+
+	while (true) {
+		if (current == NULL_IDX || path == finish || path == NULL_IDX)
+			return true;
+
+		if (getNode(current) != getNode(path))
+			return false;
+
+		current = getNextInSequence(current);
+		path = getNextInSequence(path);
+	}
+}
+
+static PassageMarkerList *getAnchors(PassageMarkerI marker, Node * nodeA,
+				     Node * nodeB)
+{
+	PassageMarkerI current, next;
+	Node *twinA = getTwinNode(nodeA);
+	Node *twinB = getTwinNode(nodeB);
+	PassageMarkerList *result = NULL;
+
+	current = marker;
+	while (current != NULL_IDX) {
+		next = getNextInSequence(current);
+		if (getNode(current) == nodeA && getNode(next) == nodeB) {
+			result = newPassageMarkerList(next, result);
+		}
+		if (getNode(current) == twinB && getNode(next) == twinA) {
+			result =
+			    newPassageMarkerList(getTwinMarker(current),
+						 result);
+		}
+		current = next;
+	}
+
+	return result;
+}
+
+static void destroyPassageMarkerList(PassageMarkerList ** list)
+{
+	PassageMarkerList *ptr;
+
+	while (*list != NULL) {
+		ptr = *list;
+		*list = ptr->next;
+		deallocatePassageMarkerList(ptr);
+	}
+}
+
+static void remapEmptyPathMarkersOntoMiddlePathDevious(PassageMarkerI emptyPath,
+						       PassageMarkerI targetPath)
+{
+	PassageMarkerI marker, newMarker, previousMarker, pathMarker;
+	Node *start = getNode(getPreviousInSequence(emptyPath));
+	Node *finish = getNode(emptyPath);
+	PassageMarkerList *anchors = getAnchors(targetPath, start, finish);
+	PassageMarkerList *currentAnchor;
+	boolean untouchable = false;
+	Coordinate markerStart;
+
+	velvetLog("DEVIOUS %li\t%li\t%li\t%li\n", (long) markerCount(finish),
+	       (long) getNodeID(finish), (long) arcCount(finish),
+	       (long) arcCount(getTwinNode(finish)));
+
+	for (marker = getMarker(finish); marker != NULL_IDX;
+	     marker = getNextInNode(marker)) {
+		newMarker = getPreviousInSequence(marker);
+
+		if (getNode(newMarker) != start)
+			continue;
+
+
+		for (currentAnchor = anchors; currentAnchor != NULL;
+		     currentAnchor = currentAnchor->next)
+			if (markerFollowsPath
+			    (marker, currentAnchor->marker, targetPath,
+			     finish)) {
+				untouchable = true;
+				break;
+			}
+
+		if (untouchable)
+			continue;
+
+		markerStart = getPassageMarkerStart(marker);
+		for (pathMarker = targetPath;
+		     getNode(pathMarker) != finish;
+		     pathMarker = getNextInSequence(pathMarker)) {
+			previousMarker = newMarker;
+			newMarker =
+			    addUncertainPassageMarker
+			    (getPassageMarkerSequenceID(marker),
+			     getNode(pathMarker));
+			setPassageMarkerStatus(newMarker,
+					       getPassageMarkerStatus
+					       (marker));
+			setPassageMarkerStart(newMarker, markerStart);
+			setPassageMarkerFinish(newMarker, markerStart);
+			setNextInSequence(previousMarker, newMarker);
+			setPreviousInSequence(previousMarker, newMarker);
+
+			setStartOffset(newMarker, 0);
+			setFinishOffset(newMarker, 0);
+		}
+
+		setNextInSequence(newMarker, marker);
+		setPreviousInSequence(newMarker, marker);
+	}
+
+	destroyPassageMarkerList(&anchors);
+}
+
+static boolean markerLeadsToArc(PassageMarkerI marker, Node * nodeA,
+				Node * nodeB)
+{
+	PassageMarkerI current, next;
+	Node *twinA = getTwinNode(nodeA);
+	Node *twinB = getTwinNode(nodeB);
+
+	current = marker;
+	while (current != NULL_IDX) {
+		next = getNextInSequence(current);
+		if (getNode(current) == nodeA && getNode(next) == nodeB)
+			return true;
+		if (getNode(current) == twinB && getNode(next) == twinA)
+			return true;
+		current = next;
+	}
+
+	return false;
+}
+
+static void
+remapEmptyPathOntoMiddlePath(PassageMarkerI emptyPath,
+			     PassageMarkerI targetPath)
+{
+	Node *start = getNode(getPreviousInSequence(emptyPath));
+	Node *finish = getNode(emptyPath);
+
+	// Remapping markers
+	if (!markerLeadsToArc(targetPath, start, finish)) {
+		remapEmptyPathArcsOntoMiddlePathSimple(emptyPath,
+						       targetPath);
+		remapEmptyPathMarkersOntoMiddlePathSimple(emptyPath,
+							  targetPath);
+	} else {
+		remapEmptyPathMarkersOntoMiddlePathDevious(emptyPath,
+							   targetPath);
+	}
+
+	//Remap times and previous(if necessary)
+	if (getNodePrevious(finish) == start)
+		remapNodeTimesOntoForwardMiddlePath(finish, targetPath);
+
+	if (getNodePrevious(getTwinNode(start)) == getTwinNode(finish))
+		remapNodeTimesOntoTwinMiddlePath(finish, targetPath);
+}
+
+static void reduceSlowNodes(PassageMarkerI slowMarker, Node * finish)
+{
+	PassageMarkerI marker;
+
+	for (marker = slowMarker; getNode(marker) != finish;
+	     marker = getNextInSequence(marker)) {
+		reduceNode(getNode(marker));
+	}
+}
+
+static void destroyPaths()
+{
+	PassageMarkerI marker;
+
+	while (slowPath != NULL_IDX) {
+		marker = slowPath;
+		slowPath = getNextInSequence(marker);
+		destroyPassageMarker(marker);
+	}
+
+	while (fastPath != NULL_IDX) {
+		marker = fastPath;
+		fastPath = getNextInSequence(marker);
+		destroyPassageMarker(marker);
+	}
+}
+
+static Coordinate mapDistancesOntoPaths()
+{
+	PassageMarkerI marker;
+	Coordinate totalDistance = 0;
+
+	marker = slowPath;
+	while (!isTerminal(marker)) {
+		marker = getNextInSequence(marker);
+		setPassageMarkerStart(marker, totalDistance);
+		totalDistance += getNodeLength(getNode(marker));
+		setPassageMarkerFinish(marker, totalDistance);
+	}
+
+	totalDistance = 0;
+	marker = fastPath;
+	while (!isTerminal(marker)) {
+		marker = getNextInSequence(marker);
+		setPassageMarkerStart(marker, totalDistance);
+		totalDistance += getNodeLength(getNode(marker));
+		setPassageMarkerFinish(marker, totalDistance);
+	}
+
+	return totalDistance;
+}
+
+static boolean markerLeadsToNode(PassageMarkerI marker, Node * node)
+{
+	PassageMarkerI currentMarker;
+
+	for (currentMarker = marker; currentMarker != NULL_IDX;
+	     currentMarker = getNextInSequence(currentMarker))
+		if (getNode(currentMarker) == node)
+			return true;
+
+	return false;
+}
+
+static void transferNodeData(Node * source, Node * target)
+{
+	Arc *arc;
+	Node *twinSource = getTwinNode(source);
+	Node *twinTarget = getTwinNode(target);
+	Node *destination;
+
+	// Time & Outward references
+	if (getNodePrevious(source) == source) {
+		setNodeTime(target, getNodeTime(source));
+		setNodePrevious(target, target);
+	}
+
+	if (getNodeTime(twinSource) == -1);
+	else if (getNodePrevious(twinSource) == twinSource) {
+		setNodeTime(twinTarget, getNodeTime(twinSource));
+		setNodePrevious(twinTarget, twinTarget);
+	} else if (getNodeTime(twinTarget) == -1
+		   || getNodeTime(twinSource) < getNodeTime(twinTarget)
+		   || (getNodeTime(twinSource) == getNodeTime(twinTarget)
+		       && !isPreviousToNode(twinTarget, twinSource))) {
+		setNodeTime(twinTarget, getNodeTime(twinSource));
+		setNodePrevious(getNodePrevious(twinSource), twinTarget);
+	}
+
+	if (getNodePrevious(twinTarget) == source)
+		setNodePrevious(target, twinTarget);
+
+	// Inward references:
+	for (arc = getArc(source); arc != NULL; arc = getNextArc(arc)) {
+		destination = getDestination(arc);
+		if (getNodePrevious(destination) == source)
+			setNodePrevious(target, destination);
+	}
+
+	// Fib Heap refs
+	remapNodeFibHeapReferencesOntoNode(source, target);
+	remapNodeFibHeapReferencesOntoNode(twinSource, twinTarget);
+
+	// Starting point
+	if (startingNode == source)
+		startingNode = target;
+	else if (startingNode == twinSource)
+		startingNode = twinTarget;
+
+	if (getNode(slowPath) == twinSource)
+		slowPath = getNextInSequence(slowPath);
+	if (getNode(fastPath) == twinSource)
+		fastPath = getNextInSequence(fastPath);
+
+	// Next node 
+	if (source == activeNode) {
+		activeNode = target;
+		todo =
+		    &todoLists[getNodeID(activeNode) + nodeCount(graph)];
+	}
+	concatenateTodoLists(target, source);
+
+	if (twinSource == activeNode) {
+		activeNode = twinTarget;
+		todo =
+		    &todoLists[getNodeID(activeNode) + nodeCount(graph)];
+	}
+}
+
+// Replaces two consecutive nodes into a single equivalent node
+// The extra memory is freed
+static void concatenateNodesAndVaccinate(Node * nodeA, Node * nodeB,
+					 Graph * graph)
+{
+	PassageMarkerI marker, tmpMarker;
+	Node *twinA = getTwinNode(nodeA);
+	Node *twinB = getTwinNode(nodeB);
+	Arc *arc;
+
+	//velvetLog("Concatenating nodes %ld and %ld\n", getNodeID(nodeA), getNodeID(nodeB));
+	// Arc management:
+	// Freeing useless arcs
+	while (getArc(nodeA) != NULL)
+		destroyArc(getArc(nodeA), graph);
+
+	// Correct arcs
+	for (arc = getArc(nodeB); arc != NULL; arc = getNextArc(arc)) {
+		if (getDestination(arc) != twinB)
+			createAnalogousArc(nodeA, getDestination(arc), arc, graph);
+		else
+			createAnalogousArc(nodeA, twinA, arc, graph);
+	}
+
+	// Passage marker management in node A:
+	for (marker = getMarker(nodeA); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (isTerminal(marker))
+			incrementFinishOffset(marker,
+					      getNodeLength(nodeB));
+
+	// Swapping new born passageMarkers from B to A
+	for (marker = getMarker(nodeB); marker != NULL_IDX; marker = tmpMarker) {
+		tmpMarker = getNextInNode(marker);
+
+		if (isInitial(marker)) {
+			extractPassageMarker(marker);
+			transposePassageMarker(marker, nodeA);
+			incrementStartOffset(marker, getNodeLength(nodeA));
+		} else
+			disconnectNextPassageMarker(getPreviousInSequence
+						    (marker), graph);
+	}
+
+	// Read starts
+	concatenateReadStarts(nodeA, nodeB, graph);
+
+	// Descriptor management 
+	appendDescriptors(nodeA, nodeB);
+
+	// Update uniqueness:
+	setUniqueness(nodeA, getUniqueness(nodeA) || getUniqueness(nodeB));
+
+#ifndef SINGLE_COV_CAT
+	Category cat;
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		// Update virtual coverage
+		incrementVirtualCoverage(nodeA, cat,
+					 getVirtualCoverage(nodeB, cat));
+		// Update virtual coverage
+		incrementOriginalVirtualCoverage(nodeA, cat,
+						 getOriginalVirtualCoverage(nodeB, cat));
+	}
+#else
+	incrementVirtualCoverage(nodeA, getVirtualCoverage(nodeB));
+#endif
+
+	// Freeing gobbled node
+	destroyNode(nodeB, graph);
+}
+
+static void simplifyNode(Node * node)
+{
+	Node *twin = getTwinNode(node);
+	Node *destination, *twinDestination;
+
+	if (!hasSingleArc(node))
+		return;
+
+	destination = getDestination(getArc(node));
+	twinDestination = getTwinNode(destination);
+
+	while (hasSingleArc(node)
+	       && hasSingleArc(twinDestination)
+	       && destination != twin && destination != node) {
+		transferNodeData(destination, node);
+		concatenateNodesAndVaccinate(node, destination, graph);
+
+		if (!hasSingleArc(node))
+			return;
+		destination = getDestination(getArc(node));
+		twinDestination = getTwinNode(destination);
+	}
+
+}
+
+static void concatenatePathNodes(PassageMarkerI pathStart)
+{
+	PassageMarkerI pathMarker;
+
+	//velvetLog("Removing null loops\n");
+	for (pathMarker = pathStart; pathMarker != NULL_IDX;
+	     pathMarker = getNextInSequence(pathMarker)) {
+		simplifyNode(getNode(pathMarker));
+	}
+}
+
+#define SLOW_TO_FAST true
+#define FAST_TO_SLOW false
+
+static void cleanUpRedundancy()
+{
+	PassageMarkerI slowMarker = getNextInSequence(slowPath);
+	PassageMarkerI fastMarker = getNextInSequence(fastPath);
+	Coordinate slowLength, fastLength;
+	Coordinate fastConstraint = 0;
+	Coordinate slowConstraint = 0;
+	Coordinate finalLength;
+	Node *slowNode, *fastNode;
+
+	//velvetLog("Correcting new redundancy\n");
+	mapSlowOntoFast();
+	finalLength = mapDistancesOntoPaths();
+
+	while (slowMarker != NULL_IDX && fastMarker != NULL_IDX) {
+		if (isTerminal(slowMarker))
+			slowLength = finalLength;
+		else {
+			slowLength =
+			    slowToFastMapping[getPassageMarkerFinish
+					      (slowMarker) - 1];
+			if (slowLength < slowConstraint)
+				slowLength = slowConstraint;
+		}
+
+		fastLength = getPassageMarkerFinish(fastMarker) - 1;
+		if (fastLength < fastConstraint)
+			fastLength = fastConstraint;
+
+		slowNode = getNode(slowMarker);
+		fastNode = getNode(fastMarker);
+
+		if (slowNode == fastNode) {
+			if (fastLength > slowLength)
+				slowConstraint = fastLength;
+			else if (fastLength < slowLength)
+				fastConstraint = slowLength;
+
+			slowMarker = getNextInSequence(slowMarker);
+			fastMarker = getNextInSequence(fastMarker);
+		} else if (slowNode == getTwinNode(fastNode)) {
+			if (fastLength > slowLength)
+				slowConstraint = fastLength;
+			else if (fastLength < slowLength)
+				fastConstraint = slowLength;
+
+			slowMarker = getNextInSequence(slowMarker);
+			fastMarker = getNextInSequence(fastMarker);
+			foldSymmetricalNode(fastNode);
+		} else if (markerLeadsToNode(slowMarker, fastNode)) {
+			reduceSlowNodes(slowMarker, fastNode);
+			remapEmptyPathOntoMiddlePath(fastMarker,
+						     slowMarker);
+			while (getNode(slowMarker) != fastNode)
+				slowMarker = getNextInSequence(slowMarker);
+		} else if (markerLeadsToNode(fastMarker, slowNode)) {
+			remapEmptyPathOntoMiddlePath(slowMarker,
+						     fastMarker);
+			while (getNode(fastMarker) != slowNode)
+				fastMarker = getNextInSequence(fastMarker);
+		} else if (slowLength == fastLength) {
+			remapNodeOntoNeighbour(slowNode, slowMarker,
+					       fastNode, fastMarker);
+			slowMarker = getNextInSequence(slowMarker);
+			fastMarker = getNextInSequence(fastMarker);
+		} else if (slowLength < fastLength) {
+			remapBackOfNodeOntoNeighbour(fastNode, fastMarker,
+						     slowNode, slowMarker,
+						     FAST_TO_SLOW);
+			slowMarker = getNextInSequence(slowMarker);
+		} else {
+			remapBackOfNodeOntoNeighbour(slowNode, slowMarker,
+						     fastNode, fastMarker,
+						     SLOW_TO_FAST);
+			fastMarker = getNextInSequence(fastMarker);
+		}
+
+		fflush(stdout);
+	}
+
+	//velvetLog("Done with path\n");
+
+	while (!isInitial(slowPath))
+		slowPath = getPreviousInSequence(slowPath);
+	while (!isInitial(fastPath))
+		fastPath = getPreviousInSequence(fastPath);
+
+	//velvetLog("Concatenation\n");
+
+	// Freeing up memory  
+	if (slowMarker != NULL_IDX)
+		concatenatePathNodes(slowPath);
+	else
+		concatenatePathNodes(fastPath);
+
+	//velvetLog("Vaccinatting\n");
+
+	destroyPaths();
+
+	// Cleaning up silly structures
+	//vaccinatePath(&returnValue);
+
+	//velvetLog("Clean up done\n");
+	//fflush(stdout);
+}
+
+static boolean pathContainsReference(PassageMarkerI path) {
+	PassageMarkerI marker, marker2;
+
+	for (marker = getNextInSequence(path); !isTerminal(marker);
+	     marker = getNextInSequence(marker))
+		for (marker2 = getMarker(getNode(marker)); marker2 != NULL_IDX; marker2 = getNextInNode(marker2))
+			if (marker2 != marker && sequenceCategories[getAbsolutePassMarkerSeqID(marker2) - 1] == REFERENCE)
+				return true;
+
+	return false;
+
+}
+
+static void comparePaths(Node * destination, Node * origin)
+{
+	IDnum slowLength, fastLength;
+	Node *fastNode, *slowNode;
+	IDnum i;
+	PassageMarkerI marker;
+
+	//Measure lengths
+	slowLength = fastLength = 0;
+	fastNode = destination;
+	slowNode = origin;
+
+	while (fastNode != slowNode) {
+		if (getNodeTime(fastNode) > getNodeTime(slowNode)) {
+			fastLength++;
+			fastNode = getNodePrevious(fastNode);
+		} else if (getNodeTime(fastNode) < getNodeTime(slowNode)) {
+			slowLength++;
+			slowNode = getNodePrevious(slowNode);
+		} else if (isPreviousToNode(slowNode, fastNode)) {
+			while (fastNode != slowNode) {
+				fastLength++;
+				fastNode = getNodePrevious(fastNode);
+			}
+		} else if (isPreviousToNode(fastNode, slowNode)) {
+			while (slowNode != fastNode) {
+				slowLength++;
+				slowNode = getNodePrevious(slowNode);
+			}
+		} else {
+			fastLength++;
+			fastNode = getNodePrevious(fastNode);
+			slowLength++;
+			slowNode = getNodePrevious(slowNode);
+		}
+
+		if (slowLength > MAXNODELENGTH
+		    || fastLength > MAXNODELENGTH)
+			return;
+	}
+
+	if (fastLength == 0)
+		return;
+
+	//Backtracking to record actual paths
+	fastPath = addUncertainPassageMarker(1, destination);
+	setPassageMarkerStatus(fastPath, true);
+
+	for (i = 0; i < fastLength; i++) {
+		marker =
+		    addUncertainPassageMarker(1,
+					      getNodePrevious(getNode
+							      (fastPath)));
+		setPassageMarkerStatus(marker, true);
+		connectPassageMarkers(marker, fastPath, graph);
+		fastPath = marker;
+	}
+
+	slowPath = addUncertainPassageMarker(2, destination);
+	setPassageMarkerStatus(slowPath, true);
+
+	marker = addUncertainPassageMarker(2, origin);
+	setPassageMarkerStatus(marker, true);
+	connectPassageMarkers(marker, slowPath, graph);
+	slowPath = marker;
+
+	for (i = 0; i < slowLength; i++) {
+		marker =
+		    addUncertainPassageMarker(2,
+					      getNodePrevious(getNode
+							      (slowPath)));
+		setPassageMarkerStatus(marker, true);
+		connectPassageMarkers(marker, slowPath, graph);
+		slowPath = marker;
+	}
+
+	// Avoid merging parallel Reference sequences
+	if (pathContainsReference(fastPath) && pathContainsReference(slowPath)) {
+		destroyPaths();
+		return;
+	}
+	//Extract sequences
+	if (!extractSequence(fastPath, fastSequence)
+	    || !extractSequence(slowPath, slowSequence)) {
+		destroyPaths();
+		return;
+	}
+	//Compare sequences
+	if (compareSequences(fastSequence, slowSequence)) {
+		cleanUpRedundancy();
+		return;
+	}
+	//velvetLog("\tFinished comparing paths, changes made\n");
+	destroyPaths();
+}
+
+static void tourBusArc(Node * origin, Arc * arc, Time originTime)
+{
+	Node *destination = getDestination(arc);
+	Time arcTime, totalTime, destinationTime;
+	IDnum nodeIndex = getNodeID(destination) + nodeCount(graph);
+	Node *oldPrevious = previous[nodeIndex];
+
+	if (oldPrevious == origin || getNodeStatus(destination) == 1)
+		return;
+
+	arcTime =
+	    ((Time) getNodeLength(origin)) / ((Time) getMultiplicity(arc));
+	totalTime = originTime + arcTime;
+
+	destinationTime = times[nodeIndex];
+
+	if (destinationTime == -1) {
+		setNodeTime(destination, totalTime);
+		dheapNodes[nodeIndex] =
+		    insertNodeIntoDHeap(dheap, totalTime, destination);
+		previous[nodeIndex] = origin;
+		return;
+	} else if (destinationTime > totalTime) {
+		if (dheapNodes[nodeIndex] == NULL) {
+			//velvetLog("Already expanded though\n");
+			return;
+		}
+
+		setNodeTime(destination, totalTime);
+		replaceKeyInDHeap(dheap, dheapNodes[nodeIndex], totalTime);
+		previous[nodeIndex] = origin;
+
+		comparePaths(destination, oldPrevious);
+		return;
+	} else {
+		if (destinationTime == getNodeTime(origin)
+		    && isPreviousToNode(destination, origin)) {
+			return;
+		}
+
+		comparePaths(destination, origin);
+	}
+}
+
+static void initializeTodoLists()
+{
+	IDnum index;
+	Node *node;
+	Arc *arc;
+	Ticket *tkt;
+	IDnum nodes = nodeCount(graph);
+	Ticket **currentList;
+	Ticket *currentTicket, *tmp;
+	Node *destination;
+
+	velvetLog("Initializing todo lists\n");
+
+	for (index = -nodes; index <= nodes; index++) {
+		node = getNodeInGraph(graph, index);
+		if (node == NULL)
+			continue;
+
+		currentList = &todoLists[index + nodes];
+		*currentList = NULL;
+
+		for (arc = getArc(node); arc != NULL;
+		     arc = getNextArc(arc)) {
+			destination = getDestination(arc);
+
+			if (destination == node)
+				continue;
+
+			tkt = newTicket();
+			tkt->id_a = getNodeID(destination);
+
+			currentTicket = *currentList;
+			if (currentTicket == NULL
+			    || currentTicket->id_a > tkt->id_a) {
+				tkt->next = currentTicket;
+				*currentList = tkt;
+				continue;
+			}
+
+			while (currentTicket->next != NULL
+			       && currentTicket->next->id_a < tkt->id_a)
+				currentTicket = currentTicket->next;
+
+			tmp = currentTicket->next;
+			currentTicket->next = tkt;
+			tkt->next = tmp;
+		}
+	}
+
+	velvetLog("Done with initilization\n");
+}
+
+static void tourBusNode(Node * node)
+{
+	Arc *arc;
+	Node *destination;
+	Time nodeTime = getNodeTime(node);
+	IDnum id;
+
+	dbgCounter++;
+	if (dbgCounter % 10000 == 0) {
+		velvetLog("%li / %li nodes visited\n", (long) dbgCounter, (long) nodeCount(graph));
+		fflush(stdout);
+	}
+
+	setSingleNodeStatus(node, 2);
+	activeNode = node;
+	todo = &todoLists[getNodeID(activeNode) + nodeCount(graph)];
+	done = NULL;
+
+	while ((id = nextTodoTicket()) != 0) {
+		destination = getNodeInGraph(graph, id);
+
+		// Node doesn't exist anymore
+		if (destination == NULL)
+			continue;
+
+		arc = getArcBetweenNodes(activeNode, destination, graph);
+
+		// Arc does not exist for some reason (?)
+		if (arc == NULL)
+			continue;
+
+		tourBusArc(activeNode, arc, nodeTime);
+	}
+
+	freeDoneTickets();
+}
+
+static Coordinate getTipLength(Node * node)
+{
+	Node *current = getTwinNode(node);
+	Coordinate length = 0;
+
+	if (simpleArcCount(current) > 1)
+		return getNodeLength(node);
+
+	while (current != NULL && simpleArcCount(getTwinNode(current)) < 2
+	       && simpleArcCount(current) < 2) {
+		length += getNodeLength(current);
+		current = getDestination(getArc(current));
+	}
+
+	return length;
+}
+
+void clipTipsHard(Graph * graph, boolean conserveLong)
+{
+	IDnum index;
+	Node *current, *twin;
+	boolean modified = true;
+	int Wordlength = getWordLength(graph);
+	PassageMarkerI marker;
+
+	velvetLog("Clipping short tips off graph, drastic\n");
+
+	while (modified) {
+		modified = false;
+		for (index = 1; index <= nodeCount(graph); index++) {
+			current = getNodeInGraph(graph, index);
+
+			if (current == NULL)
+				continue;
+	
+			if (conserveLong && getMarker(current))
+				continue;
+
+			twin = getTwinNode(current);
+
+			if (getArc(current) == NULL
+			    && getTipLength(current) < 2 * Wordlength) {
+				while ((marker = getMarker(current))) {
+					if (!isInitial(marker)
+					    && !isTerminal(marker))
+						deleteNextPassageMarker
+						    (getPreviousInSequence
+						     (marker), graph);
+					destroyPassageMarker(marker);
+				}
+				destroyNode(current, graph);
+				modified = true;
+			} else if (getArc(twin) == NULL
+				   && getTipLength(twin) <
+				   2 * Wordlength) {
+				while ((marker = getMarker(current))) {
+					if (!isInitial(marker)
+					    && !isTerminal(marker))
+						deleteNextPassageMarker
+						    (getPreviousInSequence
+						     (marker), graph);
+					destroyPassageMarker(marker);
+				}
+				destroyNode(twin, graph);
+				modified = true;
+			}
+		}
+	}
+
+	concatenateGraph(graph);
+	velvetLog("%li nodes left\n", (long) nodeCount(graph));
+}
+
+static void tourBus(Node * startingPoint)
+{
+	Node *currentNode = startingPoint;
+	IDnum nodeID = getNodeID(startingPoint) + nodeCount(graph);
+
+	//velvetLog("Tour bus from node %ld...\n", (long) getNodeID(startingPoint));
+
+	times[nodeID] = 0;
+	previous[nodeID] = currentNode;
+
+	while (currentNode != NULL) {
+		dheapNodes[getNodeID(currentNode) + nodeCount(graph)] =
+		    NULL;
+		tourBusNode(currentNode);
+		currentNode = removeNextNodeFromDHeap(dheap);
+	}
+}
+
+void correctGraph(Graph * argGraph, ShortLength * argSequenceLengths, Category * argSequenceCategories, boolean conserveLong)
+{
+	IDnum nodes;
+	IDnum index;
+	double *FmatrixMem;
+
+	//Setting global params
+	graph = argGraph;
+	WORDLENGTH = getWordLength(graph);
+	sequenceLengths = argSequenceLengths;
+	sequenceCategories = argSequenceCategories;
+	dbgCounter = 0;
+	// Done with global params
+
+	velvetLog("Correcting graph with cutoff %f\n", MAXDIVERGENCE);
+
+	nodes = nodeCount(graph);
+
+	// Allocating memory
+	times = mallocOrExit(2 * nodes + 1, Time);
+	previous = mallocOrExit(2 * nodes + 1, Node *);
+	dheapNodes = mallocOrExit(2 * nodes + 1, DFibHeapNode *);
+
+	for (index = 0; index < (2 * nodeCount(graph) + 1); index++) {
+		times[index] = -1;
+		previous[index] = NULL;
+		dheapNodes[index] = NULL;
+	}
+
+	dheap = newDFibHeap();
+
+	fastSequence = newTightString(MAXREADLENGTH);
+	slowSequence = newTightString(MAXREADLENGTH);
+	fastToSlowMapping = callocOrExit(MAXREADLENGTH + 1, Coordinate);
+	slowToFastMapping = callocOrExit(MAXREADLENGTH + 1, Coordinate);
+	Fmatrix = mallocOrExit(MAXREADLENGTH + 1, double *);
+	FmatrixMem = callocOrExit((MAXREADLENGTH + 1) * (MAXREADLENGTH + 1), double);
+	for (index = 0; index < MAXREADLENGTH + 1; index++)
+		Fmatrix[index] = FmatrixMem + index * (MAXREADLENGTH + 1);
+
+	eligibleStartingPoints = mallocOrExit(2 * nodes + 1, IDnum);
+	progressStatus = callocOrExit(2 * nodes + 1, boolean);
+	todoLists = callocOrExit(2 * nodes + 1, Ticket *);
+	//Done with memory 
+
+	resetNodeStatus(graph);
+	determineEligibleStartingPoints();
+	initializeTodoLists();
+	activateArcLookupTable(graph);
+
+	while ((startingNode = nextStartingPoint()) != NULL) {
+		//velvetLog("Going through the cycle...\n");
+		tourBus(startingNode);
+		updateNodeStatus(startingNode);
+	}
+
+	deactivateArcLookupTable(graph);
+	concatenateGraph(graph);
+
+	clipTipsHard(graph, conserveLong);
+
+	//Deallocating globals
+	free(times);
+	free(previous);
+	free(dheapNodes);
+	destroyDHeap(dheap);
+
+	destroyTightString(fastSequence);
+	destroyTightString(slowSequence);
+	free(fastToSlowMapping);
+	free(slowToFastMapping);
+	free(Fmatrix);
+	free(FmatrixMem);
+
+	free(eligibleStartingPoints);
+	free(progressStatus);
+	free(todoLists);
+
+	if (ticketMemory != NULL)
+		destroyRecycleBin(ticketMemory);
+
+	free(sequenceLengths);
+	//Done deallocating
+}
+
+void setMaxReadLength(int value)
+{
+	if (value < 0) {
+		velvetLog("Negative branch length %i!\n", value);
+		velvetLog("Exiting...\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+	MAXREADLENGTH = value;
+	MAXNODELENGTH = 2 * value;
+}
+
+void setMaxGaps(int value)
+{
+	if (value < 0) {
+		velvetLog("Negative max gap count %i!\n", value);
+		velvetLog("Exiting...\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+	MAXGAPS = value;
+}
+
+void setMaxDivergence(double value)
+{
+	if (value < 0 || value > 1) {
+		velvetLog("Divergence rate %lf out of bounds [0,1]!\n",
+		       value);
+		velvetLog("Exiting...\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+	MAXDIVERGENCE = value;
+}