bio-velvet_underground 0.0.1

data/ext/src/src/graph.c

@@ -0,0 +1,3983 @@
+/*
+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 <string.h>
+
+#include "globals.h"
+#include "graph.h"
+#include "recycleBin.h"
+#include "tightString.h"
+#include "passageMarker.h"
+#include "utility.h"
+#include "kmer.h"
+
+#define ADENINE 0
+#define CYTOSINE 1
+#define GUANINE 2
+#define THYMINE 3
+
+struct arc_st {
+	Arc *twinArc;		// 64
+	Arc *next;		// 64
+	Arc *previous;		// 64
+	Arc *nextInLookupTable;	// 64
+	Node *destination;	// 64
+	IDnum multiplicity;	// 32
+}  ATTRIBUTE_PACKED;	// 352 Total
+
+struct node_st {
+	Node *twinNode;		// 64
+	Arc *arc;		// 64
+	Descriptor *descriptor;	// 64
+	PassageMarkerI marker;	// 32
+	IDnum length;	// 32
+#ifndef SINGLE_COV_CAT
+	IDnum virtualCoverage[CATEGORIES];	// 32 * 2
+	IDnum originalVirtualCoverage[CATEGORIES];	// 32 * 2
+#else
+	IDnum virtualCoverage;	// 32 * 2
+#endif
+	IDnum ID;		// 32
+	IDnum arcCount;		// 32
+	boolean status;		// 1
+	boolean uniqueness;	// 1
+} ATTRIBUTE_PACKED;	// 418 Total
+
+struct shortReadMarker_st {
+	IDnum position;
+	IDnum readID;
+	ShortLength offset;
+} ATTRIBUTE_PACKED;
+
+struct gapMarker_st {
+	GapMarker *next;
+	IDnum position;
+	IDnum length;
+} ATTRIBUTE_PACKED;
+
+struct graph_st {
+	Node **nodes;
+	Arc **arcLookupTable;
+	ShortReadMarker **nodeReads;
+	IDnum *nodeReadCounts;
+	GapMarker **gapMarkers;
+	Coordinate insertLengths[CATEGORIES + 1];
+	double insertLengths_var[CATEGORIES + 1];
+	IDnum sequenceCount;
+	IDnum nodeCount;
+	int wordLength;
+	boolean double_stranded;
+};
+
+static RecycleBin *arcMemory = NULL;
+static RecycleBin *nodeMemory = NULL;
+static RecycleBin *gapMarkerMemory = NULL;
+
+#define BLOCKSIZE 50
+#define GAPBLOCKSIZE 10000
+
+Arc *allocateArc()
+{
+	if (arcMemory == NULL)
+		arcMemory = newRecycleBin(sizeof(Arc), BLOCKSIZE);
+
+	return allocatePointer(arcMemory);
+}
+
+void deallocateArc(Arc * arc)
+{
+	deallocatePointer(arcMemory, arc);
+}
+
+Node *allocateNode()
+{
+	if (nodeMemory == NULL)
+		nodeMemory = newRecycleBin(sizeof(Node), BLOCKSIZE);
+
+	return (Node *) allocatePointer(nodeMemory);
+}
+
+void deallocateNode(Node * node)
+{
+	deallocatePointer(nodeMemory, node);
+}
+
+// Returns the twin node of a given node
+Node *getTwinNode(Node * node)
+{
+	return node->twinNode;
+}
+
+// Inserts new passage marker in the marker list of destination node
+void insertPassageMarker(PassageMarkerI marker, Node * destination)
+{
+	setTopOfTheNode(marker);
+	setNextInNode(marker, destination->marker);
+	destination->marker = marker;
+}
+
+// Returns the length of the node's descriptor list
+Coordinate getNodeLength(Node * node)
+{
+	return node->length;
+}
+
+// Returns the number of nodes in the graph
+IDnum nodeCount(Graph * graph)
+{
+	return graph->nodeCount;
+}
+
+// returns the number of sequences used to buid the graph
+IDnum sequenceCount(Graph * graph)
+{
+	return graph->sequenceCount;
+}
+
+// Creates an arc from node origin to node destination.
+// If this arc already exists, increments its multiplicity by 1.
+Arc *createArc(Node * originNode, Node * destinationNode, Graph * graph)
+{
+	Arc *arc, *twinArc;
+	Node *destinationTwin;
+	IDnum lookupIndex;
+
+	if (originNode == NULL || destinationNode == NULL)
+		return NULL;
+
+//      velvetLog("Connecting nodes %i -> %i\n", originNode->ID, destinationNode->ID);
+
+	arc = getArcBetweenNodes(originNode, destinationNode, graph);
+
+	if (arc != NULL) {
+		arc->multiplicity++;
+		arc->twinArc->multiplicity++;
+		return arc;
+	}
+	// If not found
+#ifdef _OPENMP
+	#pragma omp critical
+#endif
+	arc = allocateArc();
+	arc->destination = destinationNode;
+	arc->multiplicity = 1;
+	arc->previous = NULL;
+	arc->next = originNode->arc;
+	if (originNode->arc != NULL)
+		originNode->arc->previous = arc;
+	originNode->arc = arc;
+	originNode->arcCount++;
+
+	destinationTwin = destinationNode->twinNode;
+
+	// Hairpin case
+	if (destinationTwin == originNode) {
+		arc->multiplicity++;
+		arc->twinArc = arc;
+		if (graph->arcLookupTable != NULL) {
+			lookupIndex =
+			    2 * originNode->ID + destinationNode->ID +
+			    3 * graph->nodeCount;
+			arc->nextInLookupTable =
+			    graph->arcLookupTable[lookupIndex];
+			graph->arcLookupTable[lookupIndex] = arc;
+		}
+		return arc;
+	}
+
+#ifdef _OPENMP
+	#pragma omp critical
+#endif
+	twinArc = allocateArc();
+	twinArc->destination = originNode->twinNode;
+	twinArc->multiplicity = 1;
+	twinArc->previous = NULL;
+	twinArc->next = destinationTwin->arc;
+	if (destinationTwin->arc != NULL)
+		destinationTwin->arc->previous = twinArc;
+	destinationTwin->arc = twinArc;
+	destinationTwin->arcCount++;
+
+	arc->twinArc = twinArc;
+	twinArc->twinArc = arc;
+
+	if (graph->arcLookupTable != NULL) {
+		lookupIndex =
+		    2 * originNode->ID + destinationNode->ID +
+		    3 * graph->nodeCount;
+		arc->nextInLookupTable =
+		    graph->arcLookupTable[lookupIndex];
+		graph->arcLookupTable[lookupIndex] = arc;
+
+		lookupIndex =
+		    -2 * destinationNode->ID - originNode->ID +
+		    3 * graph->nodeCount;
+		twinArc->nextInLookupTable =
+		    graph->arcLookupTable[lookupIndex];
+		graph->arcLookupTable[lookupIndex] = twinArc;
+	}
+	return arc;
+}
+
+void createAnalogousArc(Node * originNode, Node * destinationNode,
+			Arc * refArc, Graph * graph)
+{
+	Arc *arc, *twinArc;
+	Node *destinationTwin;
+	IDnum lookupIndex;
+
+	if (originNode == NULL || destinationNode == NULL)
+		return;
+
+//      velvetLog("Connecting nodes %i -> %i\n", originNode->ID, destinationNode->ID);
+
+	arc = getArcBetweenNodes(originNode, destinationNode, graph);
+
+	if (arc != NULL) {
+		if (refArc->twinArc != refArc) {
+			arc->multiplicity += getMultiplicity(refArc);
+			arc->twinArc->multiplicity +=
+			    getMultiplicity(refArc);
+		} else {
+			arc->multiplicity += getMultiplicity(refArc) / 2;
+			arc->twinArc->multiplicity +=
+			    getMultiplicity(refArc) / 2;
+		}
+		return;
+	}
+	// If not found
+	arc = allocateArc();
+	arc->destination = destinationNode;
+	arc->multiplicity = getMultiplicity(refArc);
+	arc->previous = NULL;
+	arc->next = originNode->arc;
+	if (originNode->arc != NULL)
+		originNode->arc->previous = arc;
+	originNode->arc = arc;
+	originNode->arcCount++;
+
+	destinationTwin = destinationNode->twinNode;
+
+	// Hairpin case
+	if (destinationTwin == originNode) {
+		arc->twinArc = arc;
+		if (refArc->twinArc != refArc)
+			arc->multiplicity *= 2;
+
+		if (graph->arcLookupTable != NULL) {
+			lookupIndex =
+			    2 * originNode->ID + destinationNode->ID
+			    + 3 * graph->nodeCount;
+			arc->nextInLookupTable =
+			    graph->arcLookupTable[lookupIndex];
+			graph->arcLookupTable[lookupIndex] = arc;
+		}
+		return;
+	}
+
+	twinArc = allocateArc();
+	twinArc->destination = originNode->twinNode;
+	twinArc->multiplicity = getMultiplicity(refArc);
+	twinArc->previous = NULL;
+	twinArc->next = destinationTwin->arc;
+	if (destinationTwin->arc != NULL)
+		destinationTwin->arc->previous = twinArc;
+	destinationTwin->arc = twinArc;
+	destinationTwin->arcCount++;
+
+	arc->twinArc = twinArc;
+	twinArc->twinArc = arc;
+
+	if (graph->arcLookupTable != NULL) {
+		lookupIndex =
+		    2 * originNode->ID + destinationNode->ID +
+		    3 * graph->nodeCount;
+		arc->nextInLookupTable =
+		    graph->arcLookupTable[lookupIndex];
+		graph->arcLookupTable[lookupIndex] = arc;
+
+		lookupIndex =
+		    -2 * destinationNode->ID - originNode->ID +
+		    3 * graph->nodeCount;
+		twinArc->nextInLookupTable =
+		    graph->arcLookupTable[lookupIndex];
+		graph->arcLookupTable[lookupIndex] = twinArc;
+	}
+}
+
+Arc *getArcBetweenNodes(Node * originNode, Node * destinationNode,
+			Graph * graph)
+{
+	Arc *arc;
+	Node *twinDestination, *twinOrigin;
+
+	if (originNode == NULL || destinationNode == NULL)
+		return NULL;
+
+	if (graph->arcLookupTable != NULL) {
+		for (arc =
+		     graph->arcLookupTable[2 * originNode->ID +
+					   destinationNode->ID +
+					   3 * graph->nodeCount];
+		     arc != NULL; arc = arc->nextInLookupTable) {
+			if (arc->destination == destinationNode) {
+				return arc;
+			}
+		}
+		return NULL;
+	}
+
+	twinDestination = destinationNode->twinNode;
+	if (originNode->arcCount <= twinDestination->arcCount) {
+		for (arc = originNode->arc; arc != NULL; arc = arc->next)
+			if (arc->destination == destinationNode)
+				return arc;
+		return NULL;
+	}
+
+	twinOrigin = originNode->twinNode;
+	for (arc = twinDestination->arc; arc != NULL; arc = arc->next)
+		if (arc->destination == twinOrigin)
+			return arc->twinArc;
+	return NULL;
+}
+
+void destroyArc(Arc * arc, Graph * graph)
+{
+	Node *origin, *destination;
+	Arc *twinArc;
+	Arc *currentArc;
+	IDnum lookupIndex;
+
+	if (arc == NULL)
+		return;
+
+	twinArc = arc->twinArc;
+	origin = twinArc->destination->twinNode;
+	destination = arc->destination->twinNode;
+
+	//velvetLog("Destroying arc %p\n", arc);
+
+	// Removing arc from list
+	if (origin->arc == arc) {
+		origin->arc = arc->next;
+		if (origin->arc != NULL)
+			origin->arc->previous = NULL;
+	} else {
+		arc->previous->next = arc->next;
+		if (arc->next != NULL)
+			arc->next->previous = arc->previous;
+	}
+
+	origin->arcCount--;
+
+	if (destination == origin) {
+		if (graph->arcLookupTable != NULL) {
+			lookupIndex =
+			    2 * origin->ID - destination->ID +
+			    3 * graph->nodeCount;
+			currentArc = graph->arcLookupTable[lookupIndex];
+			if (currentArc == arc)
+				graph->arcLookupTable[lookupIndex] =
+				    arc->nextInLookupTable;
+			else {
+				while (currentArc->nextInLookupTable !=
+				       arc)
+					currentArc =
+					    currentArc->nextInLookupTable;
+
+				currentArc->nextInLookupTable =
+				    twinArc->nextInLookupTable;
+			}
+		}
+
+		deallocateArc(arc);
+		return;
+	}
+	// Removing arc's twin from list
+	if (destination->arc == twinArc) {
+		destination->arc = twinArc->next;
+		if (destination->arc != NULL)
+			destination->arc->previous = NULL;
+	} else {
+		twinArc->previous->next = twinArc->next;
+		if (twinArc->next != NULL)
+			twinArc->next->previous = twinArc->previous;
+	}
+
+	destination->arcCount--;
+
+	if (graph->arcLookupTable != NULL) {
+		lookupIndex =
+		    2 * origin->ID - destination->ID +
+		    3 * graph->nodeCount;
+		currentArc = graph->arcLookupTable[lookupIndex];
+		if (currentArc == arc)
+			graph->arcLookupTable[lookupIndex] =
+			    arc->nextInLookupTable;
+		else {
+			while (currentArc->nextInLookupTable != arc)
+				currentArc = currentArc->nextInLookupTable;
+
+			currentArc->nextInLookupTable =
+			    arc->nextInLookupTable;
+		}
+
+		lookupIndex =
+		    2 * destination->ID - origin->ID +
+		    3 * graph->nodeCount;
+		currentArc = graph->arcLookupTable[lookupIndex];
+		if (currentArc == twinArc)
+			graph->arcLookupTable[lookupIndex] =
+			    twinArc->nextInLookupTable;
+		else {
+			while (currentArc->nextInLookupTable != twinArc)
+				currentArc = currentArc->nextInLookupTable;
+
+			currentArc->nextInLookupTable =
+			    twinArc->nextInLookupTable;
+		}
+	}
+	// Freeing memory
+	deallocateArc(arc);
+	deallocateArc(twinArc);
+}
+
+void destroyNode(Node * node, Graph * graph)
+{
+	Node *twin = node->twinNode;
+	IDnum ID = node->ID;
+	IDnum index;
+
+	//velvetLog("Destroying %d\n and twin %d\n", getNodeID(node), getNodeID(twin));
+
+	if (ID < 0)
+		ID = -ID;
+
+	// Node arcs:
+	while (node->arc != NULL)
+		destroyArc(node->arc, graph);
+	while (twin->arc != NULL)
+		destroyArc(twin->arc, graph);
+
+	// Descriptors
+	free(node->descriptor);
+	free(twin->descriptor);
+
+	// Passage markers
+	while (node->marker != NULL_IDX)
+		destroyPassageMarker(node->marker);
+
+	// Reads starts
+	if (graph->nodeReads != NULL) {
+		index = ID + graph->nodeCount;
+		free(graph->nodeReads[index]);
+		graph->nodeReads[index] = NULL;
+		graph->nodeReadCounts[index] = 0;
+
+		index = -ID + graph->nodeCount;
+		free(graph->nodeReads[index]);
+		graph->nodeReads[index] = NULL;
+		graph->nodeReadCounts[index] = 0;
+	}
+
+	graph->nodes[ID] = NULL;
+	deallocateNode(node);
+	deallocateNode(twin);
+}
+
+int outDegree(Node * node)
+{
+	int result = 0;
+	Arc *arc = node->arc;
+	while (arc != NULL) {
+		result += arc->multiplicity;
+		arc = arc->next;
+	}
+
+	return result;
+}
+
+int simpleArcCount(Node * node)
+{
+	return node->arcCount;
+}
+
+int arcCount(Node * node)
+{
+	int result = 0;
+	Arc *arc;
+
+	if (node == NULL)
+		return result;
+
+	arc = node->arc;
+	while (arc != NULL) {
+		result++;
+		if (arc->destination == node->twinNode)
+			result++;
+		arc = arc->next;
+	}
+
+	return result;
+
+}
+
+static Nucleotide getNucleotideInDescriptor(Descriptor * descriptor,
+					    Coordinate i)
+{
+	Descriptor *fourMer = descriptor + i / 4;
+
+	switch (i % 4) {
+	case 0:
+		return (*fourMer & 3);
+	case 1:
+		return (*fourMer & 12) >> 2;
+	case 2:
+		return (*fourMer & 48) >> 4;
+	case 3:
+		return (*fourMer & 192) >> 6;
+	}
+	return 0;
+}
+
+Nucleotide getNucleotideInNode(Node * node, Coordinate index) {
+        return getNucleotideInDescriptor(node->descriptor, index);
+}
+
+PassageMarkerI getMarker(Node * node)
+{
+	return node->marker;
+}
+
+void setMarker(Node * node, PassageMarkerI marker)
+{
+	if (node == NULL)
+		return;
+
+	if (marker == NULL_IDX) {
+		node->marker = NULL_IDX;
+		node->twinNode->marker = NULL_IDX;
+		return;
+	}
+
+	node->marker = marker;
+	setTopOfTheNode(marker);
+	node->twinNode->marker = getTwinMarker(marker);
+	setTopOfTheNode(getTwinMarker(marker));
+}
+
+void setNodeStatus(Node * node, boolean status)
+{
+	node->status = status;
+	node->twinNode->status = status;
+}
+
+void setSingleNodeStatus(Node * node, boolean status)
+{
+	node->status = status;
+}
+
+boolean getNodeStatus(Node * node)
+{
+	if (node == NULL)
+		return false;
+	return node->status;
+}
+
+IDnum getNodeID(Node * node)
+{
+	if (node == NULL)
+		return 0;
+
+	return node->ID;
+}
+
+void resetNodeStatus(Graph * graph)
+{
+	IDnum nodeIndex;
+	Node *node;
+
+	for (nodeIndex = 1; nodeIndex <= graph->nodeCount; nodeIndex++) {
+		node = graph->nodes[nodeIndex];
+		if (node == NULL)
+			continue;
+
+		node->status = false;
+		node->twinNode->status = false;
+	}
+}
+
+Node *getNodeInGraph(Graph * graph, IDnum nodeID)
+{
+	if (nodeID == 0)
+		return NULL;
+	else if (nodeID > 0)
+		return graph->nodes[nodeID];
+	else if (graph->nodes[-nodeID] == NULL)
+		return NULL;
+	else
+		return graph->nodes[-nodeID]->twinNode;
+}
+
+Arc *getArc(Node * node)
+{
+	return node->arc;
+}
+
+Arc *getNextArc(Arc * arc)
+{
+	return arc->next;
+}
+
+IDnum getMultiplicity(Arc * arc)
+{
+	if (arc == NULL)
+		return 0;
+
+	return arc->multiplicity;
+}
+
+Node *getOrigin(Arc * arc)
+{
+	if (arc == NULL)
+		return NULL;
+
+	return arc->twinArc->destination->twinNode;
+}
+
+Node *getDestination(Arc * arc)
+{
+	if (arc == NULL)
+		return NULL;
+
+	return arc->destination;
+}
+
+IDnum markerCount(Node * node)
+{
+	IDnum count = 0;
+	PassageMarkerI marker;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		count++;
+
+	return count;
+}
+
+void appendNodeSequence(Node * node, TightString * sequence,
+			Coordinate writeIndex)
+{
+	Coordinate i;
+	Nucleotide nucleotide;
+
+	//velvetLog("Getting sequence from node %d of length %d (%d)\n", getNodeID(node), getNodeLength(node), getLength(nodeLabel));
+
+	for (i = 0; i < getNodeLength(node); i++) {
+		nucleotide =
+		    getNucleotideInDescriptor(node->descriptor, i);
+		writeNucleotideAtPosition(nucleotide, i + writeIndex,
+					  sequence);
+	}
+}
+
+static void writeNucleotideInDescriptor(Nucleotide nucleotide,
+					Descriptor * descriptor,
+					Coordinate i)
+{
+	Descriptor *fourMer = descriptor + i / 4;
+	switch (i % 4) {
+	case 3:
+		*fourMer &= 63;
+		*fourMer += nucleotide << 6;
+		return;
+	case 2:
+		*fourMer &= 207;
+		*fourMer += nucleotide << 4;
+		return;
+	case 1:
+		*fourMer &= 243;
+		*fourMer += nucleotide << 2;
+		return;
+	case 0:
+		*fourMer &= 252;
+		*fourMer += nucleotide;
+	}
+}
+
+static inline Descriptor *mergeDescriptors(Descriptor * descr,
+					   Coordinate destinationLength,
+					   Descriptor * copy,
+					   Coordinate sourceLength,
+					   size_t arrayLength)
+{
+	Descriptor *readPtr, *writePtr;
+	Descriptor readCopy;
+	int readOffset, writeOffset;
+	Descriptor *new = callocOrExit(arrayLength, Descriptor);
+	Coordinate index;
+
+	readPtr = descr;
+	readCopy = *readPtr;
+	writePtr = new;
+	writeOffset = 0;
+	for (index = 0; index < destinationLength; index++) {
+		(*writePtr) >>= 2;
+		(*writePtr) += (readCopy & 3) << 6;
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			readPtr++;
+			if (index < destinationLength - 1)
+				readCopy = *readPtr;
+			writeOffset = 0;
+		}
+	}
+
+	readPtr = copy;
+	readCopy = *readPtr;
+	readOffset = 0;
+	for (index = 0; index < sourceLength; index++) {
+		(*writePtr) >>= 2;
+		(*writePtr) += (readCopy & 3) << 6;
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			writeOffset = 0;
+		}
+
+		readOffset++;
+		if (readOffset == 4) {
+			readPtr++;
+			if (index < sourceLength - 1)
+				readCopy = *readPtr;
+			readOffset = 0;
+		}
+	}
+
+	if (writeOffset != 0) {
+		while (writeOffset != 4) {
+			(*writePtr) >>= 2;
+			writeOffset++;
+		}
+	}
+
+	return new;
+}
+
+static void addBufferToDescriptor(Node * node, Coordinate length)
+{
+	Descriptor *descr;
+	Coordinate newLength;
+	size_t arrayLength;
+	Node *twinNode;
+	Coordinate index;
+	Descriptor *old_descriptor;
+
+	if (node == NULL)
+		return;
+
+	twinNode = node->twinNode;
+	descr = node->descriptor;
+
+	// Amendments for empty descriptors
+	if (descr == NULL) {
+		arrayLength = length / 4;
+		if (length % 4 != 0)
+			arrayLength++;
+
+		node->descriptor = callocOrExit(arrayLength, Descriptor);
+		node->length = length;
+		twinNode->descriptor =
+		    callocOrExit(arrayLength, Descriptor);
+		twinNode->length = length;
+		return;
+	}
+
+	newLength = node->length + length;
+	arrayLength = newLength / 4;
+	if (newLength % 4 != 0)
+		arrayLength++;
+
+	// Merging forward descriptors
+	node->descriptor =
+	    reallocOrExit(node->descriptor, arrayLength, Descriptor);
+
+	for (index = node->length; index < newLength; index++)
+		writeNucleotideInDescriptor(ADENINE, node->descriptor,
+					    index);
+	node->length = newLength;
+
+	// Merging reverse descriptors
+	old_descriptor = twinNode->descriptor;
+	twinNode->descriptor = callocOrExit(arrayLength, Descriptor);
+	for (index = 0; index < twinNode->length; index++)
+		writeNucleotideInDescriptor(getNucleotideInDescriptor
+					    (old_descriptor, index),
+					    twinNode->descriptor,
+					    index + length);
+	for (index = 0; index < length; index++)
+		writeNucleotideInDescriptor(THYMINE, twinNode->descriptor,
+					    index);
+	free(old_descriptor);
+	twinNode->length = newLength;
+}
+
+void appendDescriptors(Node * destination, Node * source)
+{
+	Descriptor *copy;
+	Descriptor *twinCopy;
+	Descriptor *descr;
+	Descriptor *twinDescr;
+	Coordinate newLength, destinationLength, sourceLength;
+	size_t arrayLength;
+	Descriptor *new;
+	Node *twinDestination;
+
+	if (source == NULL || destination == NULL)
+		return;
+
+	twinDestination = destination->twinNode;
+	descr = destination->descriptor;
+	twinDescr = twinDestination->descriptor;
+	copy = source->descriptor;
+	twinCopy = source->twinNode->descriptor;
+
+	// Amendments for empty descriptors
+	if (getNodeLength(source) == 0)
+		return;
+	if (getNodeLength(destination) == 0) {
+		destination->descriptor = copy;
+		twinDestination->descriptor = twinCopy;
+		source->descriptor = NULL;
+		source->twinNode->descriptor = NULL;
+		destination->length = source->length;
+		destination->twinNode->length = source->length;
+		source->length = 0;
+		source->twinNode->length = 0;
+		return;
+	}
+
+	destinationLength = destination->length;
+	sourceLength = source->length;
+	newLength = destinationLength + sourceLength;
+	arrayLength = newLength / 4;
+	if (newLength % 4 != 0)
+		arrayLength++;
+
+	// Merging forward descriptors
+	new =
+	    mergeDescriptors(descr, destinationLength, copy, sourceLength,
+			     arrayLength);
+	free(descr);
+	destination->descriptor = new;
+	destination->length = newLength;
+
+	// Merging reverse descriptors
+	new =
+	    mergeDescriptors(twinCopy, sourceLength, twinDescr,
+			     destinationLength, arrayLength);
+	free(twinDescr);
+	twinDestination->descriptor = new;
+	twinDestination->length = newLength;
+}
+
+static void catDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength) 
+{
+	Coordinate index;
+	Nucleotide nucleotide;
+
+	for (index = 0; index < sourceLength; index++) {
+		nucleotide = getNucleotideInDescriptor(copy, index);
+		writeNucleotideInDescriptor(nucleotide, descr, index + destinationLength);
+	}
+}
+
+static void reverseCatDescriptors(Descriptor * descr, Coordinate destinationLength, Descriptor * copy, Coordinate sourceLength, Coordinate totalLength) 
+{
+	Coordinate shift = totalLength - destinationLength - sourceLength;
+	Coordinate index;
+	Nucleotide nucleotide;
+
+	for (index = 0; index < sourceLength; index++) {
+		nucleotide = getNucleotideInDescriptor(copy, index);
+		writeNucleotideInDescriptor(nucleotide, descr, index + shift);
+	}
+}
+
+void directlyAppendDescriptors(Node * destination, Node * source, Coordinate totalLength)
+{
+	Descriptor *copy;
+	Descriptor *twinCopy;
+	Descriptor *descr;
+	Descriptor *twinDescr;
+	Coordinate destinationLength, sourceLength;
+
+	if (source == NULL || destination == NULL)
+		return;
+
+	descr = destination->descriptor;
+	twinDescr = destination->twinNode->descriptor;
+	copy = source->descriptor;
+	twinCopy = source->twinNode->descriptor;
+
+	// Amendments for empty descriptors
+	if (getNodeLength(source) == 0)
+		return;
+
+	destinationLength = destination->length;
+	sourceLength = source->length;
+
+	// Merging forward descriptors
+	catDescriptors(descr, destinationLength, copy, sourceLength);
+
+	// Merging reverse descriptors
+	reverseCatDescriptors(twinDescr, destinationLength, twinCopy, sourceLength, totalLength);
+
+	destination->length += source->length;
+	destination->twinNode->length += source->length;
+}
+
+static void copyDownDescriptor(Descriptor ** writePtr, int *writeOffset,
+			       Descriptor * source, Coordinate length)
+{
+	Descriptor *readPtr = source;
+	Descriptor readCopy = *readPtr;
+	int readOffset = 0;
+	Coordinate index;
+
+	for (index = 0; index < length; index++) {
+		(**writePtr) >>= 2;
+		(**writePtr) += (readCopy & 3) << 6;
+		readCopy >>= 2;
+
+		(*writeOffset)++;
+		if (*writeOffset == 4) {
+			(*writePtr)++;
+			*writeOffset = 0;
+		}
+
+		readOffset++;
+		if (readOffset == 4) {
+			readPtr++;
+			if (index < length - 1)
+				readCopy = *readPtr;
+			readOffset = 0;
+		}
+	}
+}
+
+static void copyDownSequence(Descriptor ** writePtr, int *writeOffset,
+			     TightString * sequence, Coordinate start,
+			     Coordinate finish, int WORDLENGTH)
+{
+	boolean forward = (start < finish);
+	Coordinate sourceLength = finish - start;
+	Coordinate index;
+	Nucleotide nucleotide;
+
+	if (!forward)
+		sourceLength *= -1;
+
+	for (index = 0; index < sourceLength; index++) {
+		if (forward)
+			nucleotide =
+			    getNucleotide(start + WORDLENGTH - 1 + index,
+					  sequence);
+		else
+			nucleotide =
+#ifndef COLOR
+			    3 - getNucleotide(start - index - 1, sequence);
+#else
+			    getNucleotide(start - index - 1, sequence);
+#endif
+
+		(**writePtr) >>= 2;
+		(**writePtr) += nucleotide << 6;
+
+		(*writeOffset)++;
+		if (*writeOffset == 4) {
+			(*writePtr)++;
+			*writeOffset = 0;
+		}
+	}
+}
+
+static Descriptor *appendSequenceToDescriptor(Descriptor * descr,
+					      Coordinate nodeLength,
+					      PassageMarkerI marker,
+					      TightString *sequences,
+					      int WORDLENGTH,
+					      size_t arrayLength,
+					      boolean downStream)
+{
+	int writeOffset = 0;
+	Descriptor *new = callocOrExit(arrayLength, Descriptor);
+	Descriptor *writePtr = new;
+	TightString *sequence;
+	IDnum sequenceID = getPassageMarkerSequenceID(marker);
+	Coordinate start = getPassageMarkerStart(marker);
+	Coordinate finish = getPassageMarkerFinish(marker);
+
+	if (sequenceID > 0)
+		sequence = getTightStringInArray(sequences, sequenceID - 1);
+	else
+		sequence = getTightStringInArray(sequences, -sequenceID - 1);
+
+	if (downStream)
+		copyDownDescriptor(&writePtr, &writeOffset, descr,
+				   nodeLength);
+
+	copyDownSequence(&writePtr, &writeOffset, sequence, start, finish,
+			 WORDLENGTH);
+
+	if (!downStream)
+		copyDownDescriptor(&writePtr, &writeOffset, descr,
+				   nodeLength);
+
+	if (writeOffset != 0) {
+		while (writeOffset != 4) {
+			(*writePtr) >>= 2;
+			writeOffset++;
+		}
+	}
+
+	return new;
+}
+
+void appendSequence(Node * node, TightString * reads,
+		    PassageMarkerI guide, Graph * graph)
+{
+	Descriptor *descr;
+	Descriptor *twinDescr;
+	Coordinate newLength, nodeLength, sourceLength;
+	size_t arrayLength;
+	Descriptor *new;
+	Node *twinNode;
+
+	if (node == NULL)
+		return;
+
+	twinNode = node->twinNode;
+	descr = node->descriptor;
+	twinDescr = twinNode->descriptor;
+	nodeLength = node->length;
+	sourceLength = getPassageMarkerLength(guide);
+
+	// Amendments for empty descriptors
+	if (sourceLength == 0)
+		return;
+
+	newLength = nodeLength + sourceLength;
+	arrayLength = newLength / 4;
+	if (newLength % 4 != 0)
+		arrayLength++;
+
+	// Merging forward descriptors
+	new =
+	    appendSequenceToDescriptor(descr, nodeLength, guide, reads,
+				       getWordLength(graph), arrayLength,
+				       true);
+	free(descr);
+	node->descriptor = new;
+	node->length = newLength;
+
+	// Merging reverse descriptors
+	new =
+	    appendSequenceToDescriptor(twinDescr, nodeLength,
+				       getTwinMarker(guide), reads,
+				       getWordLength(graph), arrayLength,
+				       false);
+	free(twinDescr);
+	twinNode->descriptor = new;
+	twinNode->length = newLength;
+}
+
+void setMultiplicity(Arc * arc, IDnum mult)
+{
+	arc->multiplicity = mult;
+	arc->twinArc->multiplicity = mult;
+}
+
+// Reshuffles the graph->nodes array to remove NULL pointers
+// Beware that node IDs are accordingly reshuffled (all pointers remain valid though)
+void renumberNodes(Graph * graph)
+{
+	IDnum nodeIndex;
+	Node *currentNode;
+	IDnum counter = 0;
+	IDnum nodes = graph->nodeCount;
+	IDnum newIndex;
+
+	velvetLog("Renumbering nodes\n");
+	velvetLog("Initial node count %li\n", (long) graph->nodeCount);
+
+	for (nodeIndex = 1; nodeIndex <= nodes; nodeIndex++) {
+		currentNode = getNodeInGraph(graph, nodeIndex);
+
+		if (currentNode == NULL)
+			counter++;
+		else if (counter != 0) {
+			newIndex = nodeIndex - counter;
+			currentNode->ID = newIndex;
+			currentNode->twinNode->ID = -newIndex;
+			graph->nodes[newIndex] = currentNode;
+
+			if (graph->nodeReads != NULL) {
+				graph->nodeReads[newIndex + nodes] =
+				    graph->nodeReads[nodeIndex + nodes];
+				graph->nodeReadCounts[newIndex + nodes] =
+				    graph->nodeReadCounts[nodeIndex +
+							  nodes];
+
+				graph->nodeReads[nodeIndex + nodes] = NULL;
+				graph->nodeReadCounts[nodeIndex + nodes] =
+				    0;
+
+				graph->nodeReads[-newIndex + nodes] =
+				    graph->nodeReads[-nodeIndex + nodes];
+				graph->nodeReadCounts[-newIndex + nodes] =
+				    graph->nodeReadCounts[-nodeIndex +
+							  nodes];
+
+				graph->nodeReads[-nodeIndex + nodes] =
+				    NULL;
+				graph->nodeReadCounts[-nodeIndex + nodes] =
+				    0;
+			}
+
+			if (graph->gapMarkers != NULL) {
+				graph->gapMarkers[newIndex] =
+				    graph->gapMarkers[nodeIndex];
+				graph->gapMarkers[nodeIndex] = NULL;
+			}
+		}
+	}
+
+	// Shitfting array to the left
+	if (graph->nodeReads != NULL && counter != 0) {
+		for (nodeIndex = counter; nodeIndex <= 2 * nodes - counter;
+		     nodeIndex++) {
+			graph->nodeReads[nodeIndex - counter] =
+			    graph->nodeReads[nodeIndex];
+			graph->nodeReadCounts[nodeIndex - counter] =
+			    graph->nodeReadCounts[nodeIndex];
+		}
+	}
+
+	// Rellocating node space
+	graph->nodeCount -= counter;
+	graph->nodes =
+	    reallocOrExit(graph->nodes, graph->nodeCount + 1, Node *);
+
+	// Reallocating short read marker arrays
+	if (graph->nodeReads != NULL) {
+		graph->nodeReads =
+		    reallocOrExit(graph->nodeReads,
+			    2 * graph->nodeCount +
+			     1, ShortReadMarker *);
+		graph->nodeReadCounts =
+		    reallocOrExit(graph->nodeReadCounts,
+			    2 * graph->nodeCount + 1, IDnum);
+	}
+
+	// Reallocating gap marker table
+	if (graph->gapMarkers != NULL)
+		graph->gapMarkers = reallocOrExit(graph->gapMarkers,
+					    graph->nodeCount +
+					     1, GapMarker *);
+
+	velvetLog("Removed %li null nodes\n", (long) counter);
+}
+
+void splitNodeDescriptor(Node * source, Node * target, Coordinate offset)
+{
+	Coordinate originalLength = source->length;
+	Coordinate backLength = originalLength - offset;
+	Coordinate index;
+	Descriptor *descriptor, *new;
+	size_t arrayLength;
+	Nucleotide nucleotide;
+
+	source->length = offset;
+	source->twinNode->length = offset;
+
+	if (target != NULL) {
+		target->length = backLength;
+		target->twinNode->length = backLength;
+		free(target->descriptor);
+		free(target->twinNode->descriptor);
+		target->descriptor = NULL;
+		target->twinNode->descriptor = NULL;
+	}
+
+	if (backLength == 0)
+		return;
+
+	descriptor = source->descriptor;
+
+	arrayLength = backLength / 4;
+	if (backLength % 4 > 0)
+		arrayLength++;
+
+	if (target != NULL) {
+		// Target node .. forwards
+		new = mallocOrExit(arrayLength, Descriptor);
+		target->descriptor = new;
+		for (index = 0; index < backLength; index++) {
+			nucleotide =
+			    getNucleotideInDescriptor(descriptor, index);
+			writeNucleotideInDescriptor(nucleotide, new,
+						    index);
+		}
+	}
+	// Source node
+	for (index = backLength; index < originalLength; index++) {
+		nucleotide = getNucleotideInDescriptor(descriptor, index);
+		writeNucleotideInDescriptor(nucleotide, descriptor,
+					    index - backLength);
+	}
+
+	if (target == NULL)
+		return;
+
+	// target node other way
+	descriptor = source->twinNode->descriptor;
+	new = mallocOrExit(arrayLength, Descriptor);
+	target->twinNode->descriptor = new;
+
+	for (index = offset; index < originalLength; index++) {
+		nucleotide = getNucleotideInDescriptor(descriptor, index);
+		writeNucleotideInDescriptor(nucleotide, new,
+					    index - offset);
+	}
+}
+
+void reduceNode(Node * node)
+{
+	free(node->descriptor);
+	node->descriptor = NULL;
+	node->length = 0;
+
+	free(node->twinNode->descriptor);
+	node->twinNode->descriptor = NULL;
+	node->twinNode->length = 0;
+}
+
+// Allocate memory for an empty graph created with sequenceCount different sequences
+Graph *emptyGraph(IDnum sequenceCount, int wordLength)
+{
+	Graph *newGraph = mallocOrExit(1, Graph);
+	newGraph->sequenceCount = sequenceCount;
+	newGraph->arcLookupTable = NULL;
+	newGraph->nodeReads = NULL;
+	newGraph->nodeReadCounts = NULL;
+	newGraph->wordLength = wordLength;
+	newGraph->gapMarkers = NULL;
+	return newGraph;
+}
+
+static Descriptor *newPositiveDescriptor(IDnum sequenceID,
+					 Coordinate start,
+					 Coordinate finish,
+					 TightString *sequences,
+					 int WORDLENGTH)
+{
+	Coordinate index;
+	Nucleotide nucleotide;
+	TightString *tString = getTightStringInArray (sequences, sequenceID - 1);
+	Coordinate length = finish - start;
+	Descriptor *res;
+	size_t arrayLength = length / 4;
+
+	if (length % 4 > 0)
+		arrayLength++;
+
+	res = mallocOrExit(arrayLength, Descriptor);
+
+	for (index = 0; index < length; index++) {
+		nucleotide =
+		    getNucleotide(start + index + WORDLENGTH - 1, tString);
+		writeNucleotideInDescriptor(nucleotide, res, index);
+	}
+
+	return res;
+
+}
+
+static Descriptor *newNegativeDescriptor(IDnum sequenceID,
+					 Coordinate start,
+					 Coordinate finish,
+					 TightString *sequences,
+					 int WORDLENGTH)
+{
+	Coordinate index;
+	Nucleotide nucleotide;
+	TightString *tString = getTightStringInArray (sequences, -sequenceID - 1);
+	Coordinate length = start - finish;
+	Descriptor *res;
+	size_t arrayLength = length / 4;
+
+	if (length % 4 > 0)
+		arrayLength++;
+
+	res = mallocOrExit(arrayLength, Descriptor);
+
+	for (index = 0; index < length; index++) {
+		nucleotide = getNucleotide(start - index, tString);
+#ifndef COLOR
+		writeNucleotideInDescriptor(3 - nucleotide, res, index);
+#else
+		writeNucleotideInDescriptor(nucleotide, res, index);
+#endif
+	}
+
+	return res;
+
+}
+
+static Descriptor *newDescriptor(IDnum sequenceID, Coordinate start,
+				 Coordinate finish,
+				 TightString * sequences, int WORDLENGTH)
+{
+	if (sequenceID > 0)
+		return newPositiveDescriptor(sequenceID, start, finish,
+					     sequences, WORDLENGTH);
+	else
+		return newNegativeDescriptor(sequenceID, start, finish,
+					     sequences, WORDLENGTH);
+}
+
+// Constructor
+// Memory allocated
+Node *newNode(IDnum sequenceID, Coordinate start, Coordinate finish,
+	      Coordinate offset, IDnum ID, TightString * sequences,
+	      int WORDLENGTH)
+{
+	Node *newnd = allocateNode();
+	Node *antiNode = allocateNode();
+
+	newnd->ID = ID;
+	newnd->descriptor =
+	    newDescriptor(sequenceID, start + offset, finish + offset,
+			  sequences, WORDLENGTH);
+	newnd->arc = NULL;
+	newnd->arcCount = 0;
+	newnd->marker = NULL_IDX;
+	newnd->status = false;
+
+#ifndef SINGLE_COV_CAT
+	Category cat;
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		newnd->virtualCoverage[cat] = 0;
+		newnd->originalVirtualCoverage[cat] = 0;
+	}
+#else
+	newnd->virtualCoverage = 0;
+#endif
+
+	antiNode->ID = -ID;
+	antiNode->descriptor =
+	    newDescriptor(-sequenceID, finish + offset - 1,
+			  start + offset - 1, sequences, WORDLENGTH);
+	antiNode->arc = NULL;
+	antiNode->arcCount = 0;
+	antiNode->marker = NULL_IDX;
+	antiNode->status = false;
+
+#ifndef SINGLE_COV_CAT
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		antiNode->virtualCoverage[cat] = 0;
+		antiNode->originalVirtualCoverage[cat] = 0;
+	}
+#else
+	antiNode->virtualCoverage = 0;
+#endif
+
+	newnd->twinNode = antiNode;
+	antiNode->twinNode = newnd;
+
+	if (sequenceID > 0) {
+		newnd->length = finish - start;
+		antiNode->length = finish - start;
+	} else {
+		newnd->length = start - finish;
+		antiNode->length = start - finish;
+	}
+
+	return newnd;
+}
+
+void allocateNodeSpace(Graph * graph, IDnum nodeCount)
+{
+	graph->nodes = callocOrExit(nodeCount + 1, Node *);
+	graph->nodeCount = nodeCount;
+}
+
+boolean getUniqueness(Node * node)
+{
+	return node->uniqueness;
+}
+
+void setUniqueness(Node * node, boolean value)
+{
+	node->uniqueness = value;
+	node->twinNode->uniqueness = value;
+}
+
+Node *emptyNode()
+{
+	Node *newnd = allocateNode();
+	Node *antiNode = allocateNode();
+
+	newnd->ID = 0;
+	newnd->descriptor = NULL;
+	newnd->arc = NULL;
+	newnd->arcCount = 0;
+	newnd->marker = NULL_IDX;
+	newnd->length = 0;
+	newnd->uniqueness = false;
+
+#ifndef SINGLE_COV_CAT
+	Category cat;
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		newnd->virtualCoverage[cat] = 0;
+		newnd->originalVirtualCoverage[cat] = 0;
+	}
+#else
+	newnd->virtualCoverage = 0;
+#endif
+
+	antiNode->ID = 0;
+	antiNode->descriptor = NULL;
+	antiNode->arc = NULL;
+	antiNode->arcCount = 0;
+	antiNode->marker = NULL_IDX;
+	antiNode->length = 0;
+	antiNode->uniqueness = false;
+
+#ifndef SINGLE_COV_CAT
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		antiNode->virtualCoverage[cat] = 0;
+		antiNode->originalVirtualCoverage[cat] = 0;
+	}
+#else
+	antiNode->virtualCoverage = 0;
+#endif
+
+	newnd->twinNode = antiNode;
+	antiNode->twinNode = newnd;
+
+	return newnd;
+
+}
+
+Node *addEmptyNodeToGraph(Graph * graph, IDnum ID)
+{
+	Node *newnd = emptyNode();
+
+	newnd->ID = ID;
+	newnd->twinNode->ID = -ID;
+
+	graph->nodes[ID] = newnd;
+
+	return newnd;
+
+}
+
+#ifndef SINGLE_COV_CAT
+
+void setVirtualCoverage(Node * node, Category category,
+			Coordinate coverage)
+{
+	node->virtualCoverage[category] = coverage;
+	node->twinNode->virtualCoverage[category] =
+	    node->virtualCoverage[category];
+}
+
+void incrementVirtualCoverage(Node * node, Category category,
+			      Coordinate coverage)
+{
+	node->virtualCoverage[category] += coverage;
+	node->twinNode->virtualCoverage[category] =
+	    node->virtualCoverage[category];
+}
+
+Coordinate getVirtualCoverage(Node * node, Category category)
+{
+	return node->virtualCoverage[category];
+}
+
+Coordinate getTotalCoverage(Node * node)
+{
+	Category cat;
+	Coordinate coverage = 0;
+
+	for (cat = 0; cat < CATEGORIES; cat++)
+		coverage += node->virtualCoverage[cat];
+
+	return coverage;
+}
+
+void setOriginalVirtualCoverage(Node * node, Category category,
+				Coordinate coverage)
+{
+	node->originalVirtualCoverage[category] = coverage;
+	node->twinNode->originalVirtualCoverage[category] =
+	    node->originalVirtualCoverage[category];
+}
+
+void incrementOriginalVirtualCoverage(Node * node, Category category,
+				      Coordinate coverage)
+{
+	node->originalVirtualCoverage[category] += coverage;
+	node->twinNode->originalVirtualCoverage[category] =
+	    node->originalVirtualCoverage[category];
+}
+
+Coordinate getOriginalVirtualCoverage(Node * node, Category category)
+{
+	return node->originalVirtualCoverage[category];
+}
+
+#else
+
+void setVirtualCoverage(Node * node,
+			Coordinate coverage)
+{
+	node->virtualCoverage = coverage;
+	node->twinNode->virtualCoverage = coverage;
+}
+
+void incrementVirtualCoverage(Node * node,
+			      Coordinate coverage)
+{
+	node->virtualCoverage += coverage;
+	node->twinNode->virtualCoverage += coverage;
+}
+
+Coordinate getVirtualCoverage(Node * node)
+{
+	return node->virtualCoverage;
+}
+
+Coordinate getTotalCoverage(Node * node)
+{
+	return node->virtualCoverage;
+}
+
+#endif
+
+boolean hasSingleArc(Node * node)
+{
+	return node->arcCount == 1;
+}
+
+void activateArcLookupTable(Graph * graph)
+{
+	IDnum index;
+	Node *node;
+	Arc *arc;
+	IDnum nodes = graph->nodeCount;
+	IDnum twinOriginID, destinationID, hash;
+	Arc **table;
+
+	velvetLog("Activating arc lookup table\n");
+
+	graph->arcLookupTable = callocOrExit(6 * nodes + 1, Arc *);
+
+	table = graph->arcLookupTable;
+
+	for (index = -nodes; index <= nodes; index++) {
+		if (index == 0)
+			continue;
+
+		node = getNodeInGraph(graph, index);
+		if (node == 0)
+			continue;
+
+		for (arc = getArc(node); arc != NULL;
+		     arc = getNextArc(arc)) {
+			twinOriginID = arc->twinArc->destination->ID;
+			destinationID = arc->destination->ID;
+			hash =
+			    3 * nodes - 2 * twinOriginID + destinationID;
+			arc->nextInLookupTable = table[hash];
+			table[hash] = arc;
+		}
+	}
+
+	velvetLog("Done activating arc lookup table\n");
+}
+
+void deactivateArcLookupTable(Graph * graph)
+{
+	free(graph->arcLookupTable);
+	graph->arcLookupTable = NULL;
+}
+
+static void exportNode(FILE * outfile, Node * node, void *withSequence)
+{
+	Coordinate index;
+	Nucleotide nucleotide;
+
+	if (node == NULL)
+		return;
+
+	velvetFprintf(outfile, "NODE\t%ld\t%lld", (long) node->ID, (long long) node->length);
+
+#ifndef SINGLE_COV_CAT
+	Category cat;
+	for (cat = 0; cat < CATEGORIES; cat++)
+		velvetFprintf(outfile, "\t%lld\t%lld", (long long) node->virtualCoverage[cat],
+			(long long) node->originalVirtualCoverage[cat]);
+	velvetFprintf(outfile, "\n");
+#else
+	velvetFprintf(outfile, "\t%lld\n", (long long) node->virtualCoverage);
+#endif
+
+	if (withSequence == NULL)
+		return;
+
+	for (index = 0; index < node->length; index++) {
+		nucleotide =
+		    getNucleotideInDescriptor(node->descriptor, index);
+		switch (nucleotide) {
+		case ADENINE:
+			velvetFprintf(outfile, "A");
+			break;
+		case CYTOSINE:
+			velvetFprintf(outfile, "C");
+			break;
+		case GUANINE:
+			velvetFprintf(outfile, "G");
+			break;
+		case THYMINE:
+			velvetFprintf(outfile, "T");
+			break;
+		}
+	}
+	velvetFprintf(outfile, "\n");
+
+	for (index = 0; index < node->length; index++) {
+		nucleotide =
+		    getNucleotideInDescriptor(node->twinNode->descriptor,
+					      index);
+		switch (nucleotide) {
+		case ADENINE:
+			velvetFprintf(outfile, "A");
+			break;
+		case CYTOSINE:
+			velvetFprintf(outfile, "C");
+			break;
+		case GUANINE:
+			velvetFprintf(outfile, "G");
+			break;
+		case THYMINE:
+			velvetFprintf(outfile, "T");
+			break;
+		}
+	}
+	velvetFprintf(outfile, "\n");
+}
+
+static void exportArc(FILE * outfile, Arc * arc)
+{
+	IDnum originID, destinationID;
+	IDnum absOriginID, absDestinationID;
+
+	if (arc == NULL)
+		return;
+
+	absOriginID = originID = -arc->twinArc->destination->ID;
+	absDestinationID = destinationID = arc->destination->ID;
+
+	if (absOriginID < 0)
+		absOriginID = -absOriginID;
+	if (absDestinationID < 0)
+		absDestinationID = -absDestinationID;
+
+	if (absDestinationID < absOriginID)
+		return;
+
+	if (originID == destinationID && originID < 0)
+		return;
+
+	velvetFprintf(outfile, "ARC\t%li\t%li\t%li\n", (long) originID, (long) destinationID,
+		(long) arc->multiplicity);
+}
+
+// Merges two lists of annotations in order of increasing position (used in mergeSort mainly)
+static Arc *mergeArcLists(Arc * left, Arc * right)
+{
+	Arc *mergedList = NULL;
+	Arc *tail = NULL;
+
+	// Choose first element:
+	if (left->destination->ID <= right->destination->ID) {
+		mergedList = left;
+		tail = left;
+		left = left->next;
+	} else {
+		mergedList = right;
+		tail = right;
+		right = right->next;
+	}
+
+	// Iterate while both lists are still non empty
+	while (left != NULL && right != NULL) {
+		if (left->destination->ID <= right->destination->ID) {
+			tail->next = left;
+			left->previous = tail;
+			left = left->next;
+		} else {
+			tail->next = right;
+			right->previous = tail;
+			right = right->next;
+		}
+
+		tail = tail->next;
+	}
+
+	// Concatenate the remaining list at the end of the merged list
+	if (left != NULL) {
+		tail->next = left;
+		left->previous = tail;
+	}
+
+	if (right != NULL) {
+		tail->next = right;
+		right->previous = tail;
+	}
+
+	return mergedList;
+}
+
+static void arcMergeSort(Arc ** arcPtr, IDnum count)
+{
+
+	IDnum half = count / 2;
+	Arc *left = *arcPtr;
+	Arc *ptr = left;
+	Arc *right;
+	IDnum index;
+
+	if (count == 0 || count == 1)
+		return;
+
+	if (count == 2) {
+		if ((*arcPtr)->destination->ID >
+		    (*arcPtr)->next->destination->ID) {
+			(*arcPtr)->next->next = *arcPtr;
+			(*arcPtr)->previous = (*arcPtr)->next;
+			*arcPtr = (*arcPtr)->next;
+			(*arcPtr)->next->next = NULL;
+			(*arcPtr)->previous = NULL;
+		}
+		return;
+	}
+
+	for (index = 0; index < half - 1; index++) {
+		ptr = ptr->next;
+		if (ptr == NULL)
+			return;
+	}
+
+	right = ptr->next;
+	ptr->next = NULL;
+	right->previous = NULL;
+
+	arcMergeSort(&left, half);
+	arcMergeSort(&right, count - half);
+	*arcPtr = mergeArcLists(left, right);
+}
+
+static void sortNodeArcs(Node * node)
+{
+	Arc *arc;
+	IDnum count = 0;
+
+	for (arc = getArc(node); arc != NULL; arc = getNextArc(arc))
+		count++;
+
+	if (count == 0)
+		return;
+
+	arc = getArc(node);
+	arcMergeSort(&arc, count);
+
+	node->arc = arc;
+}
+
+// Merges two lists of annotations in order of increasing position (used in mergeSort mainly)
+static GapMarker *mergeGapMarkerLists(GapMarker * left, GapMarker * right)
+{
+	GapMarker *mergedList = NULL;
+	GapMarker *tail = NULL;
+
+	// Choose first element:
+	if (left->position <= right->position) {
+		mergedList = left;
+		tail = left;
+		left = left->next;
+	} else {
+		mergedList = right;
+		tail = right;
+		right = right->next;
+	}
+
+	// Iterate while both lists are still non empty
+	while (left != NULL && right != NULL) {
+		if (left->position <= right->position) {
+			tail->next = left;
+			left = left->next;
+		} else {
+			tail->next = right;
+			right = right->next;
+		}
+
+		tail = tail->next;
+	}
+
+	// Concatenate the remaining list at the end of the merged list
+	if (left != NULL)
+		tail->next = left;
+
+	if (right != NULL)
+		tail->next = right;
+
+	return mergedList;
+}
+
+static void gapMergeSort(GapMarker ** gapPtr, IDnum count)
+{
+
+	IDnum half = count / 2;
+	GapMarker *left = *gapPtr;
+	GapMarker *ptr = left;
+	GapMarker *right;
+	IDnum index;
+
+	if (count == 0 || count == 1)
+		return;
+
+	if (count == 2) {
+		if ((*gapPtr)->position > (*gapPtr)->next->position) {
+			(*gapPtr)->next->next = *gapPtr;
+			*gapPtr = (*gapPtr)->next;
+			(*gapPtr)->next->next = NULL;
+		}
+		return;
+	}
+
+	for (index = 0; index < half - 1; index++) {
+		ptr = ptr->next;
+		if (ptr == NULL)
+			return;
+	}
+
+	right = ptr->next;
+	ptr->next = NULL;
+
+	gapMergeSort(&left, half);
+	gapMergeSort(&right, count - half);
+	*gapPtr = mergeGapMarkerLists(left, right);
+}
+
+static void sortNodeGapMarkers(Node * node, Graph * graph)
+{
+	GapMarker *gap;
+	IDnum count = 0;
+	IDnum ID = getNodeID(node);
+
+	if (ID < 0)
+		ID = -ID;
+
+	for (gap = graph->gapMarkers[ID]; gap != NULL; gap = gap->next)
+		count++;
+
+	if (count == 0)
+		return;
+
+	gap = graph->gapMarkers[ID];
+	gapMergeSort(&gap, count);
+
+	graph->gapMarkers[ID] = gap;
+}
+
+void sortGapMarkers(Graph * graph)
+{
+	IDnum index;
+	Node *node;
+
+	if (graph->gapMarkers == NULL)
+		return;
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+		if (node)
+			sortNodeGapMarkers(node, graph);
+	}
+}
+
+void exportGraph(char *filename, Graph * graph, TightString * sequences)
+{
+	IDnum index;
+	FILE *outfile;
+	Node *node;
+	Arc *arc;
+	PassageMarkerI marker;
+	ShortReadMarker *reads;
+	IDnum readCount, readIndex;
+
+	if (graph == NULL) {
+		return;
+	}
+
+	outfile = fopen(filename, "w");
+	if (outfile == NULL) {
+		velvetLog("Couldn't open file, sorry\n");
+		return;
+	} else
+		velvetLog("Writing into graph file %s...\n", filename);
+
+	// General data
+	velvetFprintf(outfile, "%li\t%li\t%i\t%i\n", (long) graph->nodeCount,
+		(long) graph->sequenceCount, graph->wordLength, (int) graph->double_stranded);
+
+	// Node info
+	for (index = 1; index <= graph->nodeCount; index++) {
+		node = getNodeInGraph(graph, index);
+		exportNode(outfile, node, (void *) sequences);
+	}
+
+	// Arc info
+	for (index = 1; index <= graph->nodeCount; index++) {
+		node = getNodeInGraph(graph, index);
+		if (node == NULL)
+			continue;
+
+		sortNodeArcs(node);
+		sortNodeArcs(getTwinNode(node));
+
+		for (arc = node->arc; arc != NULL; arc = arc->next)
+			exportArc(outfile, arc);
+		for (arc = node->twinNode->arc; arc != NULL;
+		     arc = arc->next)
+			exportArc(outfile, arc);
+	}
+
+	// Sequence info
+	for (index = 1; index <= graph->nodeCount; index++) {
+		node = getNodeInGraph(graph, index);
+		if (node == NULL)
+			continue;
+		for (marker = node->marker; marker != NULL_IDX;
+		     marker = getNextInNode(marker))
+			exportMarker(outfile, marker, sequences,
+				     graph->wordLength);
+	}
+
+	// Node reads
+	if (readStartsAreActivated(graph)) {
+		for (index = 0; index <= graph->nodeCount * 2; index++) {
+			readCount = graph->nodeReadCounts[index];
+			if (readCount == 0)
+				continue;
+
+			velvetFprintf(outfile, "NR\t%li\t%li\n",
+				(long) (index - graph->nodeCount), (long) readCount);
+
+			reads = graph->nodeReads[index];
+			for (readIndex = 0; readIndex < readCount;
+			     readIndex++)
+				velvetFprintf(outfile, "%ld\t%lld\t%d\n",
+					(long) reads[readIndex].readID,
+					(long long) reads[readIndex].position,
+					(int) reads[readIndex].offset);
+		}
+	}
+
+	fclose(outfile);
+}
+
+Graph *importGraph(char *filename)
+{
+	FILE *file = fopen(filename, "r");
+	const int maxline = MAXLINE;
+	char line[MAXLINE];
+	Graph *graph;
+	Coordinate coverage;
+	IDnum nodeCounter, sequenceCount;
+	Node *node, *twin;
+	Arc *arc;
+	IDnum originID, destinationID, multiplicity;
+	PassageMarkerI newMarker, marker;
+	IDnum nodeID, seqID;
+	Coordinate index;
+	Coordinate start, finish;
+	Coordinate startOffset, finishOffset;
+	boolean finished = false;
+	size_t arrayLength;
+	IDnum readCount;
+	ShortReadMarker *array;
+	int wordLength, sCount;
+	ShortLength length;
+	long long_var, long_var2, long_var3;
+	long long longlong_var, longlong_var2, longlong_var3, longlong_var4;
+	short short_var;
+	char c;
+
+	if (file == NULL) 
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	velvetLog("Reading graph file %s\n", filename);
+
+	// First  line
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "Graph file incomplete");
+	sscanf(line, "%ld\t%ld\t%i\t%hi\n", &long_var, &long_var2,
+	       &wordLength, &short_var);
+	nodeCounter = (IDnum) long_var;
+	sequenceCount = (IDnum) long_var2;
+	graph = emptyGraph(sequenceCount, wordLength);
+	graph->double_stranded = (boolean) short_var;
+	resetWordFilter(wordLength);
+	allocateNodeSpace(graph, nodeCounter);
+
+	velvetLog("Graph has %ld nodes and %ld sequences\n", (long) nodeCounter,
+	       (long) sequenceCount);
+
+	if (nodeCounter == 0)
+		return graph;
+
+	// Read nodes
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "Graph file incomplete");
+	while (!finished && strncmp(line, "NODE", 4) == 0) {
+		strtok(line, "\t\n");
+		sscanf(strtok(NULL, "\t\n"), "%ld", &long_var);
+		nodeID = (IDnum) long_var;
+		node = addEmptyNodeToGraph(graph, nodeID);
+		sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+		node->length = (Coordinate) longlong_var;
+
+#ifndef SINGLE_COV_CAT
+		Category cat;
+		Coordinate originalCoverage;
+		for (cat = 0; cat < CATEGORIES; cat++) {
+			sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+			coverage = (Coordinate) longlong_var;
+			setVirtualCoverage(node, cat, coverage);
+			sscanf(strtok(NULL, "\t\n"), "%lld",
+			       &longlong_var);
+			originalCoverage = (Coordinate) longlong_var;
+			setOriginalVirtualCoverage(node, cat,
+						   originalCoverage);
+		}
+#else
+		sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+		coverage = (Coordinate) longlong_var;
+		setVirtualCoverage(node, coverage);
+#endif
+
+		arrayLength = node->length / 4;
+		if (node->length % 4 > 0)
+			arrayLength++;
+		node->descriptor =
+		    callocOrExit(arrayLength, Descriptor);
+
+		index = 0;
+		while ((c = fgetc(file)) != '\n' && c != EOF) {
+			if (c == 'A')
+				writeNucleotideInDescriptor(ADENINE,
+							    node->
+							    descriptor,
+							    index++);
+			else if (c == 'C')
+				writeNucleotideInDescriptor(CYTOSINE,
+							    node->
+							    descriptor,
+							    index++);
+			else if (c == 'G')
+				writeNucleotideInDescriptor(GUANINE,
+							    node->
+							    descriptor,
+							    index++);
+			else if (c == 'T')
+				writeNucleotideInDescriptor(THYMINE,
+							    node->
+							    descriptor,
+							    index++);
+		}
+
+		twin = node->twinNode;
+		twin->length = node->length;
+		twin->descriptor =
+		    callocOrExit(arrayLength, Descriptor);
+		index = 0;
+		while ((c = fgetc(file)) != '\n' && c != EOF) {
+			if (c == 'A')
+				writeNucleotideInDescriptor(ADENINE,
+							    twin->
+							    descriptor,
+							    index++);
+			else if (c == 'C')
+				writeNucleotideInDescriptor(CYTOSINE,
+							    twin->
+							    descriptor,
+							    index++);
+			else if (c == 'G')
+				writeNucleotideInDescriptor(GUANINE,
+							    twin->
+							    descriptor,
+							    index++);
+			else if (c == 'T')
+				writeNucleotideInDescriptor(THYMINE,
+							    twin->
+							    descriptor,
+							    index++);
+		}
+
+		if (fgets(line, maxline, file) == NULL)
+			finished = true;
+	}
+
+	// Read arcs
+	while (!finished && line[0] == 'A') {
+		sscanf(line, "ARC\t%ld\t%ld\t%ld\n", &long_var,
+		       &long_var2, &long_var3);
+		originID = (IDnum) long_var;
+		destinationID = (IDnum) long_var2;
+		multiplicity = (IDnum) long_var3;
+		arc =
+		    createArc(getNodeInGraph(graph, originID),
+			      getNodeInGraph(graph, destinationID), graph);
+		setMultiplicity(arc, multiplicity);
+		if (fgets(line, maxline, file) == NULL)
+			finished = true;
+	}
+
+	// Read sequences
+	while (!finished && line[0] != 'N') {
+		sscanf(line, "SEQ\t%ld\n", &long_var);
+		seqID = (IDnum) long_var;
+		marker = NULL_IDX;
+		if (!fgets(line, maxline, file))
+			exitErrorf(EXIT_FAILURE, true, "Graph file incomplete");
+
+		while (!finished && line[0] != 'N' && line[0] != 'S') {
+			sCount =
+			    sscanf(line, "%ld\t%lld\t%lld\t%lld\t%lld\n",
+				   &long_var, &longlong_var, &longlong_var2, &longlong_var3,
+				   &longlong_var4);
+			nodeID = (IDnum) long_var;
+			startOffset = (Coordinate) longlong_var;
+			start = (Coordinate) longlong_var2;
+			finish = (Coordinate) longlong_var3;
+			finishOffset = (Coordinate) longlong_var4;
+			if (sCount != 5) {
+				velvetLog
+				    ("ERROR: reading in graph - only %d items read for line '%s'",
+				     sCount, line);
+#ifdef DEBUG 
+				abort();
+#endif 
+				exit(1);
+			}
+			newMarker =
+			    newPassageMarker(seqID, start, finish,
+					     startOffset, finishOffset);
+			transposePassageMarker(newMarker,
+					       getNodeInGraph(graph,
+							      nodeID));
+			connectPassageMarkers(marker, newMarker, graph);
+			marker = newMarker;
+			if (fgets(line, maxline, file) == NULL)
+				finished = true;
+		}
+	}
+
+	// Node reads
+	while (!finished) {
+		sscanf(line, "NR\t%ld\t%ld\n", &long_var, &long_var2);
+		nodeID = (IDnum) long_var;
+		readCount = (IDnum) long_var2;
+		if (!readStartsAreActivated(graph))
+			activateReadStarts(graph);
+
+		graph->nodeReadCounts[nodeID + graph->nodeCount] =
+		    readCount;
+		array = mallocOrExit(readCount, ShortReadMarker);
+		graph->nodeReads[nodeID + graph->nodeCount] = array;
+
+		readCount = 0;
+		if (!fgets(line, maxline, file))
+			exitErrorf(EXIT_FAILURE, true, "Graph file incomplete");
+		while (!finished && line[0] != 'N') {
+			sscanf(line, "%ld\t%lld\t%hd\n", &long_var,
+			       &longlong_var, &short_var);
+			seqID = (IDnum) long_var;
+			startOffset = (Coordinate) longlong_var;
+			length = (ShortLength) short_var;
+			array[readCount].readID = seqID;
+			array[readCount].position = startOffset;
+			array[readCount].offset = length;
+			readCount++;
+			if (fgets(line, maxline, file) == NULL)
+				finished = true;
+		}
+	}
+
+	//velvetLog("New graph has %d nodes\n", graph->nodeCount);
+
+	fclose(file);
+	//velvetLog("Done, exiting\n");
+	return graph;
+}
+
+Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand)
+{
+	FILE *file = fopen(preGraphFilename, "r");
+	const int maxline = MAXLINE;
+	char line[MAXLINE];
+
+	Graph *graph;
+	IDnum nodeCounter, sequenceCount;
+
+	Node *node, *twin;
+	IDnum nodeID = 0;
+	Coordinate index, nodeLength;
+	char c;
+	int wordLength, wordShift;
+	size_t arrayLength;
+	short short_var;
+	long long_var, long_var2;
+	long long longlong_var;
+
+	if (file == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
+
+	velvetLog("Reading pre-graph file %s\n", preGraphFilename);
+
+	// First  line
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
+	sscanf(line, "%ld\t%ld\t%i\t%hi\n", &long_var, &long_var2,
+	       &wordLength, &short_var);
+	nodeCounter = (IDnum) long_var;
+	sequenceCount = (IDnum) long_var2;
+	*double_strand = (boolean) short_var;
+	wordShift = wordLength - 1;
+	graph = emptyGraph(sequenceCount, wordLength);
+	graph->double_stranded = *double_strand;
+	resetWordFilter(wordLength);
+	allocateNodeSpace(graph, nodeCounter);
+	velvetLog("Graph has %ld nodes and %ld sequences\n", (long) nodeCounter,
+	       (long) sequenceCount);
+
+	// Read nodes
+	if (nodeCounter == 0)
+		return graph;
+
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
+	while (line[0] == 'N') {
+		nodeID++;
+		node = addEmptyNodeToGraph(graph, nodeID);
+
+		sscanf(line, "%*s\t%*i\t%lli\n", &longlong_var);
+		node->length = (Coordinate) longlong_var;
+		nodeLength = node->length;
+		arrayLength = node->length / 4;
+		if (node->length % 4 > 0)
+			arrayLength++;
+		node->descriptor =
+		    callocOrExit(arrayLength, Descriptor);
+
+		twin = node->twinNode;
+		twin->length = nodeLength;
+		twin->descriptor =
+		    callocOrExit(arrayLength, Descriptor);
+
+
+		index = 0;
+		while ((c = getc(file)) != '\n') {
+			if (c == 'A') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(ADENINE,
+								    node->
+								    descriptor,
+								    index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(THYMINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(ADENINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'C') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(CYTOSINE,
+								    node->
+								    descriptor,
+								    index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(GUANINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(CYTOSINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'G') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(GUANINE,
+								    node->
+								    descriptor,
+								    index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(CYTOSINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(GUANINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'T') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(THYMINE,
+								    node->
+								    descriptor,
+								    index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(ADENINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(THYMINE,
+								    twin->
+								    descriptor,
+								    nodeLength - index - 1);
+#endif
+				}
+			}
+			
+			index++;
+		}
+
+		if (fgets(line, maxline, file) == NULL) {
+			fclose(file);
+			return graph;
+		}
+	}
+
+	fclose(file);
+	return graph;
+}
+
+Graph *readConnectedGraphFile(char *connectedGraphFilename, boolean * double_strand)
+{
+	FILE *file = fopen(connectedGraphFilename, "r");
+	const int maxline = MAXLINE;
+	char line[MAXLINE];
+	Coordinate coverage;
+	Arc *arc;
+	IDnum originID, destinationID, multiplicity;
+	boolean finished = false;
+	long long_var3;
+
+	Graph *graph;
+	IDnum nodeCounter, sequenceCount;
+
+	Node *node, *twin;
+	IDnum nodeID = 0;
+	Coordinate index, nodeLength;
+	char c;
+	int wordLength, wordShift;
+	size_t arrayLength;
+	short short_var;
+	long long_var, long_var2;
+	long long longlong_var;
+
+	if (file == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", connectedGraphFilename);
+
+	velvetLog("Reading connected graph file %s\n", connectedGraphFilename);
+
+	// First  line
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
+	sscanf(line, "%ld\t%ld\t%i\t%hi\n", &long_var, &long_var2,
+			&wordLength, &short_var);
+	nodeCounter = (IDnum) long_var;
+	sequenceCount = (IDnum) long_var2;
+	*double_strand = (boolean) short_var;
+	wordShift = wordLength - 1;
+	graph = emptyGraph(sequenceCount, wordLength);
+	graph->double_stranded = *double_strand;
+	resetWordFilter(wordLength);
+	allocateNodeSpace(graph, nodeCounter);
+	velvetLog("Graph has %ld nodes and %ld sequences\n", (long) nodeCounter,
+			(long) sequenceCount);
+
+	// Read nodes
+	if (nodeCounter == 0)
+		return graph;
+
+	if (!fgets(line, maxline, file))
+		exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
+	while (!finished && strncmp(line, "NODE", 4) == 0) {
+		strtok(line, "\t\n");
+		sscanf(strtok(NULL, "\t\n"), "%ld", &long_var);
+		nodeID = (IDnum) long_var;
+		node = addEmptyNodeToGraph(graph, nodeID);
+		sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+		node->length = (Coordinate) longlong_var;
+		nodeLength = node->length;
+
+#ifndef SINGLE_COV_CAT
+		Category cat;
+		Coordinate originalCoverage;
+		for (cat = 0; cat < CATEGORIES; cat++) {
+			sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+			coverage = (Coordinate) longlong_var;
+			setVirtualCoverage(node, cat, coverage);
+			sscanf(strtok(NULL, "\t\n"), "%lld",
+					&longlong_var);
+			originalCoverage = (Coordinate) longlong_var;
+			setOriginalVirtualCoverage(node, cat,
+					originalCoverage);
+		}
+#else
+		sscanf(strtok(NULL, "\t\n"), "%lld", &longlong_var);
+		coverage = (Coordinate) longlong_var;
+		setVirtualCoverage(node, coverage);
+#endif
+
+		arrayLength = node->length / 4;
+		if (node->length % 4 > 0)
+			arrayLength++;
+		node->descriptor =
+			callocOrExit(arrayLength, Descriptor);
+
+		twin = node->twinNode;
+		twin->length = node->length;
+		twin->descriptor =
+			callocOrExit(arrayLength, Descriptor);   
+
+		index = 0;
+		while ((c = getc(file)) != '\n') {
+			if (c == 'A') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(ADENINE,
+							node->
+							descriptor,
+							index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(THYMINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(ADENINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'C') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(CYTOSINE,
+							node->
+							descriptor,
+							index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(GUANINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(CYTOSINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'G') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(GUANINE,
+							node->
+							descriptor,
+							index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(CYTOSINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(GUANINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#endif
+				}
+			} else if (c == 'T') {
+				if (index - wordShift >= 0)
+					writeNucleotideInDescriptor(THYMINE,
+							node->
+							descriptor,
+							index - wordShift);
+				if (nodeLength - index - 1 >= 0) {
+#ifndef COLOR
+					writeNucleotideInDescriptor(ADENINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#else
+					writeNucleotideInDescriptor(THYMINE,
+							twin->
+							descriptor,
+							nodeLength - index - 1);
+#endif
+				}
+			}
+
+			index++;
+		}
+
+		if (fgets(line, maxline, file) == NULL) {
+			finished = true;
+		}
+	}
+
+	// Read arcs
+	while (!finished && line[0] == 'A') {
+		sscanf(line, "ARC\t%ld\t%ld\t%ld\n", &long_var,
+				&long_var2, &long_var3);
+		originID = (IDnum) long_var;
+		destinationID = (IDnum) long_var2;
+		multiplicity = (IDnum) long_var3;
+		arc =
+			createArc(getNodeInGraph(graph, originID),
+					getNodeInGraph(graph, destinationID), graph);
+		setMultiplicity(arc, multiplicity);
+		if (fgets(line, maxline, file) == NULL)
+			finished = true;
+	}
+
+	fclose(file);
+	return graph;
+}
+
+// Prints out the information relative to the topology of a node into a new file
+// Internal to exportDOTGraph()
+void DOTNode(Node * node, FILE * outfile)
+{
+	IDnum ID;
+	Arc *arc;
+	Node *otherNode;
+
+	ID = node->ID;
+	if (ID < 0)
+		return;
+
+	velvetFprintf(outfile, "\t%li [label=\"<left>|%li|<right>\"]\n", (long) ID, (long) ID);
+
+	for (arc = node->arc; arc != NULL; arc = arc->next) {
+		otherNode = arc->destination;
+		if (!(otherNode->ID >= ID || otherNode->ID <= -ID)) {
+			continue;
+		}
+
+		if (otherNode->ID > 0)
+			velvetFprintf(outfile, "\t%li:right -> %li:left\n", (long) ID,
+				(long) otherNode->ID);
+		else
+			velvetFprintf(outfile, "\t%li:right -> %li:right\n", (long) ID,
+				(long) -otherNode->ID);
+	}
+
+	for (arc = node->twinNode->arc; arc != NULL; arc = arc->next) {
+		otherNode = arc->destination;
+		if (!(otherNode->ID >= ID || otherNode->ID <= -ID)) {
+			continue;
+		}
+
+		if (otherNode->ID > 0)
+			velvetFprintf(outfile, "\t%li:left -> %li:left\n", (long) ID,
+				(long) otherNode->ID);
+		else
+			velvetFprintf(outfile, "\t%li:left -> %li:right\n", (long) ID,
+				(long) -otherNode->ID);
+	}
+}
+
+TightString *expandNode(Node * node, int WORDLENGTH)
+{
+	Nucleotide nucleotide;
+	Coordinate index;
+	TightString *tString =
+	    newTightString(node->length + WORDLENGTH - 1);
+	Node *twin = node->twinNode;
+	Coordinate length = node->length;
+
+	for (index = 0; index < WORDLENGTH; index++) {
+		nucleotide =
+		    getNucleotideInDescriptor(twin->descriptor,
+					      length - index - 1);
+#ifndef COLOR
+		writeNucleotideAtPosition(3 - nucleotide, index, tString);
+#else
+		writeNucleotideAtPosition(nucleotide, index, tString);
+#endif
+	}
+
+	for (index = 1; index < node->length; index++) {
+		nucleotide =
+		    getNucleotideInDescriptor(node->descriptor, index);
+		writeNucleotideAtPosition(nucleotide,
+					  index + WORDLENGTH - 1, tString);
+	}
+
+	return tString;
+}
+
+char *expandNodeFragment(Node * node, Coordinate contigStart,
+			 Coordinate contigFinish, int wordLength)
+{
+	Nucleotide nucleotide;
+	Coordinate index;
+	Node *twin = node->twinNode;
+	Coordinate length = contigFinish - contigStart;
+	int wordShift = wordLength - 1;
+	char *string;
+
+	if (length >= wordShift) {
+		string = callocOrExit(length + wordLength, char);
+
+		for (index = 0; index < wordShift; index++) {
+			nucleotide =
+			    getNucleotideInDescriptor(twin->descriptor,
+						      twin->length - contigStart -
+						      index - 1);
+	#ifndef COLOR
+			nucleotide = 3 - nucleotide;
+	#endif
+
+			switch (nucleotide) {
+			case ADENINE:
+				string[index] = 'A';
+				break;
+			case CYTOSINE:
+				string[index] = 'C';
+				break;
+			case GUANINE:
+				string[index] = 'G';
+				break;
+			case THYMINE:
+				string[index] = 'T';
+				break;
+			}
+
+		}
+
+		for (index = 0; index < length; index++) {
+			nucleotide =
+			    getNucleotideInDescriptor(node->descriptor,
+						      contigStart + index);
+			switch (nucleotide) {
+			case ADENINE:
+				string[index + wordShift] = 'A';
+				break;
+			case CYTOSINE:
+				string[index + wordShift] = 'C';
+				break;
+			case GUANINE:
+				string[index + wordShift] = 'G';
+				break;
+			case THYMINE:
+				string[index + wordShift] = 'T';
+				break;
+			}
+		}
+
+		string[length + wordShift] = '\0';
+	} else {
+		string = callocOrExit(length + 1, char);
+
+		for (index = 0; index < length; index++) {
+			nucleotide =
+			    getNucleotideInDescriptor(node->descriptor, contigStart + index);
+			switch (nucleotide) {
+			case ADENINE:
+				string[index] = 'A';
+				break;
+			case CYTOSINE:
+				string[index] = 'C';
+				break;
+			case GUANINE:
+				string[index] = 'G';
+				break;
+			case THYMINE:
+				string[index] = 'T';
+				break;
+			}
+		}
+
+		string[length] = '\0';
+	}
+
+	return string;
+}
+
+boolean readStartsAreActivated(Graph * graph)
+{
+	return graph->nodeReads != NULL;
+}
+
+void activateReadStarts(Graph * graph)
+{
+	graph->nodeReads =
+	    callocOrExit(2 * graph->nodeCount + 1, ShortReadMarker *);
+	graph->nodeReadCounts =
+	    callocOrExit(2 * graph->nodeCount + 1, IDnum);
+}
+
+void deactivateReadStarts(Graph * graph)
+{
+	free(graph->nodeReads);
+	free(graph->nodeReadCounts);
+
+	graph->nodeReads = NULL;
+	graph->nodeReadCounts = NULL;
+}
+
+boolean findIDnumInArray(IDnum query, IDnum * array, IDnum arrayLength)
+{
+	IDnum leftIndex = 0;
+	IDnum rightIndex = arrayLength;
+	IDnum middleIndex;
+
+	if (arrayLength == 0)
+		return false;
+
+	while (true) {
+		middleIndex = leftIndex + (rightIndex - leftIndex) / 2;
+
+		if (array[middleIndex] == query)
+			return true;
+		else if (leftIndex >= rightIndex)
+			return false;
+		else if (array[middleIndex] > query)
+			rightIndex = middleIndex;
+		else if (leftIndex == middleIndex)
+			leftIndex++;
+		else
+			leftIndex = middleIndex;
+	}
+}
+
+static inline int compareShortReadMarkers(const void *A, const void *B)
+{
+	IDnum a = ((ShortReadMarker *) A)->readID;
+	IDnum b = ((ShortReadMarker *) B)->readID;
+
+	if (a > b)
+		return 1;
+	if (a == b)
+		return 0;
+	return -1;
+}
+
+static inline int compareIDnums(const void *A, const void *B)
+{
+	IDnum a = *((IDnum *) A);
+	IDnum b = *((IDnum *) B);
+
+	if (a > b)
+		return 1;
+	if (a == b)
+		return 0;
+	return -1;
+}
+
+void incrementReadStartCount(Node * node, Graph * graph)
+{
+	graph->nodeReadCounts[node->ID + graph->nodeCount]++;
+}
+
+void createNodeReadStartArrays(Graph * graph)
+{
+	IDnum index;
+
+	if (graph->nodeReads == NULL)
+		return;
+
+	for (index = 0; index <= 2 * (graph->nodeCount); index++) {
+		if (graph->nodeReadCounts[index] != 0) {
+			graph->nodeReads[index] =
+			    mallocOrExit(graph->nodeReadCounts[index],
+				   ShortReadMarker);
+			graph->nodeReadCounts[index] = 0;
+		} else {
+			graph->nodeReads[index] = NULL;
+		}
+	}
+}
+
+void orderNodeReadStartArrays(Graph * graph)
+{
+	IDnum index;
+
+	if (graph->nodeReads == NULL)
+		return;
+
+	for (index = 0; index <= 2 * (graph->nodeCount); index++)
+		if (graph->nodeReadCounts[index] != 0)
+			qsort(graph->nodeReads[index],
+			      graph->nodeReadCounts[index],
+			      sizeof(ShortReadMarker),
+			      compareShortReadMarkers);
+}
+
+void addReadStart(Node * node, IDnum seqID, Coordinate position,
+		  Graph * graph, Coordinate offset)
+{
+	IDnum nodeIndex = getNodeID(node) + graph->nodeCount;
+
+	ShortReadMarker *array = graph->nodeReads[nodeIndex];
+	IDnum arrayLength = graph->nodeReadCounts[nodeIndex];
+
+	array[arrayLength].readID = seqID;
+	array[arrayLength].position = position;
+	array[arrayLength].offset = (ShortLength) offset;
+	// printf("node %d, seq %d, pos %ld, offset %ld\n", getNodeID(node), seqID, position, offset);
+	graph->nodeReadCounts[nodeIndex]++;
+}
+
+void blurLastShortReadMarker(Node * node, Graph * graph)
+{
+	IDnum nodeIndex = getNodeID(node) + nodeCount(graph);
+	IDnum index = graph->nodeReadCounts[nodeIndex] - 1;
+	ShortReadMarker *marker;
+
+	if (index >= 0)
+		marker = &(graph->nodeReads[nodeIndex][index]);
+	else
+		abort();
+
+	setShortReadMarkerPosition(marker, -1);
+}
+
+ShortReadMarker *commonNodeReads(Node * nodeA, Node * nodeB, Graph * graph,
+				 IDnum * length)
+{
+	IDnum targetID, targetLength, targetIndex, targetVal;
+	IDnum sourceID, sourceLength, sourceIndex, sourceVal;
+	IDnum mergeLength;
+	ShortReadMarker *mergeArray, *targetArray, *sourceArray;
+
+	if (graph->nodeReads == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	if (nodeA == NULL || nodeB == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	targetID = getNodeID(nodeA) + graph->nodeCount;
+	targetArray = graph->nodeReads[targetID];
+	targetLength = graph->nodeReadCounts[targetID];
+
+	sourceID = getNodeID(nodeB) + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+
+	if (sourceArray == NULL || targetArray == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	mergeArray =
+	    mallocOrExit(sourceLength +
+		    targetLength, ShortReadMarker);
+
+	mergeLength = 0;
+	sourceIndex = 0;
+	targetIndex = 0;
+	sourceVal = sourceArray[0].readID;
+	targetVal = targetArray[0].readID;
+
+	while (sourceIndex < sourceLength && targetIndex < targetLength) {
+		switch (compareIDnums(&sourceVal, &targetVal)) {
+		case -1:
+			mergeArray[mergeLength].readID = sourceVal;
+			mergeArray[mergeLength].position = -1;
+			mergeArray[mergeLength].offset = -1;
+			mergeLength++;
+			sourceIndex++;
+			if (sourceIndex < sourceLength)
+				sourceVal =
+				    sourceArray[sourceIndex].readID;
+			break;
+		case 0:
+			mergeArray[mergeLength].readID = sourceVal;
+			mergeArray[mergeLength].position = -1;
+			mergeArray[mergeLength].offset = -1;
+			mergeLength++;
+			sourceIndex++;
+			if (sourceIndex < sourceLength)
+				sourceVal =
+				    sourceArray[sourceIndex].readID;
+			targetIndex++;
+			if (targetIndex < targetLength)
+				targetVal =
+				    targetArray[targetIndex].readID;
+			break;
+		case 1:
+			mergeArray[mergeLength].readID = targetVal;
+			mergeArray[mergeLength].position = -1;
+			mergeArray[mergeLength].offset = -1;
+			mergeLength++;
+			targetIndex++;
+			if (targetIndex < targetLength)
+				targetVal =
+				    targetArray[targetIndex].readID;
+		}
+	}
+
+	while (sourceIndex < sourceLength) {
+		mergeArray[mergeLength].readID =
+		    sourceArray[sourceIndex].readID;
+		mergeArray[mergeLength].position = -1;
+		mergeArray[mergeLength].offset = -1;
+		mergeLength++;
+		sourceIndex++;
+	}
+
+	while (targetIndex < targetLength) {
+		mergeArray[mergeLength].readID =
+		    targetArray[targetIndex].readID;
+		mergeArray[mergeLength].position = -1;
+		mergeArray[mergeLength].offset = -1;
+		mergeLength++;
+		targetIndex++;
+	}
+
+	*length = mergeLength;
+	return mergeArray;
+}
+
+ShortReadMarker *extractFrontOfNodeReads(Node * node,
+					 Coordinate breakpoint,
+					 Graph * graph, IDnum * length,
+					 PassageMarkerI sourceMarker,
+					 ShortLength * lengths)
+{
+	IDnum sourceID;
+	IDnum mergeLength, newLength, sourceLength;
+	IDnum sourceIndex;
+	ShortReadMarker *mergeArray, *sourceArray, *newArray;
+	ShortReadMarker *mergePtr, *sourcePtr, *newPtr;
+	Coordinate finish;
+	Coordinate revBreakpoint;
+
+	if (graph->nodeReads == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	if (node == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	if (breakpoint == 0) {
+		return commonNodeReads(node,
+				       getTwinNode(getNode
+						   (getPreviousInSequence
+						    (sourceMarker))),
+				       graph, length);
+	}
+
+	sourceID = getNodeID(node) + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+
+	if (sourceArray == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	revBreakpoint = node->length - breakpoint;
+
+	mergeLength = 0;
+	newLength = 0;
+	sourcePtr = sourceArray;
+	for (sourceIndex = 0; sourceIndex < sourceLength; sourceIndex++) {
+		if (sourcePtr->position == -1) {
+			newLength++;
+			mergeLength++;
+		} else {
+			finish =
+			    sourcePtr->position - sourcePtr->offset +
+			    lengths[sourcePtr->readID - 1];
+			if (sourcePtr->position < revBreakpoint)
+				newLength++;
+			if (finish > revBreakpoint)
+				mergeLength++;
+		}
+		sourcePtr++;
+	}
+
+	newArray = mallocOrExit(newLength, ShortReadMarker);
+	mergeArray = mallocOrExit(mergeLength, ShortReadMarker);
+
+	mergePtr = mergeArray;
+	newPtr = newArray;
+	sourcePtr = sourceArray;
+	mergeLength = 0;
+	newLength = 0;
+	for (sourceIndex = 0; sourceIndex < sourceLength; sourceIndex++) {
+		if (sourcePtr->position == -1) {
+			mergePtr->readID = sourcePtr->readID;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr++;
+			mergeLength++;
+			newPtr->readID = sourcePtr->readID;
+			setShortReadMarkerPosition(newPtr, -1);
+			setShortReadMarkerOffset(newPtr, -1);
+			newPtr++;
+			newLength++;
+		} else {
+			finish =
+			    sourcePtr->position - sourcePtr->offset +
+			    lengths[sourcePtr->readID - 1];
+			if (sourcePtr->position < revBreakpoint) {
+				newPtr->readID = sourcePtr->readID;
+				setShortReadMarkerPosition(newPtr,
+							   sourcePtr->
+							   position);
+				setShortReadMarkerOffset(newPtr,
+							 sourcePtr->
+							 offset);
+				newPtr++;
+				newLength++;
+
+				// Saddle back reads:
+				if (finish > revBreakpoint) {
+					mergePtr->readID =
+					    sourcePtr->readID;
+					setShortReadMarkerPosition
+					    (mergePtr, 0);
+					setShortReadMarkerOffset(mergePtr,
+								 sourcePtr->
+								 offset +
+								 revBreakpoint
+								 -
+								 sourcePtr->
+								 position);
+					mergePtr++;
+				}
+			} else if (finish > revBreakpoint) {
+				mergePtr->readID = sourcePtr->readID;
+				setShortReadMarkerPosition(mergePtr,
+							   sourcePtr->
+							   position - revBreakpoint);
+				setShortReadMarkerOffset(mergePtr,
+							 sourcePtr->
+							 offset);
+				mergePtr++;
+				mergeLength++;
+			}
+		}
+
+		sourcePtr++;
+	}
+
+	free(sourceArray);
+	graph->nodeReads[sourceID] = newArray;
+	graph->nodeReadCounts[sourceID] = newLength;
+
+	*length = mergeLength;
+	return mergeArray;
+}
+
+ShortReadMarker *extractBackOfNodeReads(Node * node, Coordinate breakpoint,
+					Graph * graph, IDnum * length,
+					PassageMarkerI sourceMarker,
+					ShortLength  * lengths)
+{
+	IDnum sourceID;
+	IDnum mergeLength, newLength, sourceLength;
+	IDnum sourceIndex;
+	ShortReadMarker *mergeArray, *sourceArray, *newArray;
+	ShortReadMarker *mergePtr, *sourcePtr, *newPtr;
+	Coordinate finish;
+
+	if (graph->nodeReads == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	if (node == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	if (breakpoint == 0) {
+		return
+		    commonNodeReads(getNode
+				    (getPreviousInSequence(sourceMarker)),
+				    node, graph, length);
+	}
+
+	sourceID = getNodeID(node) + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+
+	if (sourceArray == NULL) {
+		*length = 0;
+		return NULL;
+	}
+
+	mergeLength = 0;
+	newLength = 0;
+	sourcePtr = sourceArray;
+	for (sourceIndex = 0; sourceIndex < sourceLength; sourceIndex++) {
+		if (sourcePtr->position == -1) {
+			mergeLength++;
+			newLength++;
+		} else {
+			finish =
+			    sourcePtr->position - sourcePtr->offset +
+			    lengths[sourcePtr->readID - 1];
+			if (sourcePtr->position < breakpoint)
+				mergeLength++;
+			if (finish > breakpoint)
+				newLength++;
+		}
+		sourcePtr++;
+	}
+
+	newArray = mallocOrExit(newLength, ShortReadMarker);
+	mergeArray = mallocOrExit(mergeLength, ShortReadMarker);
+
+	mergePtr = mergeArray;
+	newPtr = newArray;
+	sourcePtr = sourceArray;
+	for (sourceIndex = 0; sourceIndex < sourceLength; sourceIndex++) {
+		if (sourcePtr->position == -1) {
+			mergePtr->readID = sourcePtr->readID;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr++;
+
+			newPtr->readID = sourcePtr->readID;
+			setShortReadMarkerPosition(newPtr, -1);
+			setShortReadMarkerOffset(newPtr, -1);
+			newPtr++;
+
+			sourcePtr++;
+			continue;
+		} else {
+			finish =
+			    sourcePtr->position - sourcePtr->offset +
+			    lengths[sourcePtr->readID - 1];
+
+			if (sourcePtr->position < breakpoint) {
+				mergePtr->readID = sourcePtr->readID;
+				setShortReadMarkerPosition(mergePtr,
+							   sourcePtr->
+							   position);
+				setShortReadMarkerOffset(mergePtr,
+							 sourcePtr->
+							 offset);
+				mergePtr++;
+
+				// Saddle back reads:
+				if (finish > breakpoint) {
+					newPtr->readID = sourcePtr->readID;
+					setShortReadMarkerPosition(newPtr,
+								   0);
+					setShortReadMarkerOffset(newPtr,
+								 sourcePtr->
+								 offset +
+								 breakpoint
+								 -
+								 sourcePtr->
+								 position);
+					newPtr++;
+				}
+			} else if (finish > breakpoint) {
+				newPtr->readID = sourcePtr->readID;
+				setShortReadMarkerPosition(newPtr,
+							   sourcePtr->
+							   position -
+							   breakpoint);
+				setShortReadMarkerOffset(newPtr,
+							 sourcePtr->
+							 offset);
+				newPtr++;
+			}
+		}
+
+		sourcePtr++;
+	}
+
+	free(sourceArray);
+	graph->nodeReads[sourceID] = newArray;
+	graph->nodeReadCounts[sourceID] = newLength;
+
+	*length = mergeLength;
+	return mergeArray;
+}
+
+void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,
+		   Graph * graph)
+{
+	IDnum targetID, targetLength, targetIndex, targetVal;
+	IDnum sourceLength, sourceIndex, sourceVal;
+	IDnum mergeLength;
+	ShortReadMarker *sourceArray, *targetArray, *mergeArray;
+	ShortReadMarker *sourcePtr, *targetPtr, *mergePtr;
+	Coordinate targetPosition;
+	//ShortLength nodeLength = (ShortLength) getNodeLength(node);
+	ShortLength targetOffset;
+
+	if (graph->nodeReads == NULL || reads == NULL || node == NULL)
+		return;
+
+	targetID = getNodeID(node) + graph->nodeCount;
+	targetArray = graph->nodeReads[targetID];
+	targetLength = graph->nodeReadCounts[targetID];
+	targetPtr = targetArray;
+
+	sourceArray = reads;
+	sourceLength = readCount;
+	sourcePtr = sourceArray;
+
+	if (targetArray == NULL) {
+		mergeArray =
+		    mallocOrExit(sourceLength, ShortReadMarker);
+		mergePtr = mergeArray;
+
+		sourceIndex = 0;
+		while (sourceIndex < sourceLength) {
+			mergePtr->readID = sourcePtr->readID;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr++;
+			sourcePtr++;
+			sourceIndex++;
+		}
+
+		graph->nodeReads[targetID] = mergeArray;
+		graph->nodeReadCounts[targetID] = sourceLength;
+		return;
+	}
+
+	mergeArray =
+	    mallocOrExit(sourceLength +
+		    targetLength, ShortReadMarker);
+	mergePtr = mergeArray;
+
+	mergeLength = 0;
+	sourceIndex = 0;
+	targetIndex = 0;
+	sourceVal = sourcePtr->readID;
+	targetVal = targetPtr->readID;
+	targetPosition = targetPtr->position;
+	targetOffset = targetPtr->offset;
+
+	while (sourceIndex < sourceLength && targetIndex < targetLength) {
+		if (sourceVal < targetVal) {
+			mergePtr->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			sourceIndex++;
+			sourcePtr++;
+			if (sourceIndex < sourceLength)
+				sourceVal = sourcePtr->readID;
+		} else if (sourceVal == targetVal) {
+			mergePtr->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			sourceIndex++;
+			sourcePtr++;
+			if (sourceIndex < sourceLength)
+				sourceVal = sourcePtr->readID;
+			targetIndex++;
+			targetPtr++;
+			if (targetIndex < targetLength) {
+				targetVal = targetPtr->readID;
+				targetPosition = targetPtr->position;
+				targetOffset = targetPtr->offset;
+			}
+		} else {
+			mergePtr->readID = targetVal;
+			setShortReadMarkerPosition(mergePtr,
+						   targetPosition);
+			setShortReadMarkerOffset(mergePtr, targetOffset);
+			targetIndex++;
+			targetPtr++;
+			if (targetIndex < targetLength) {
+				targetVal = targetPtr->readID;
+				targetPosition = targetPtr->position;
+				targetOffset = targetPtr->offset;
+			}
+		}
+
+		mergeLength++;
+		mergePtr++;
+	}
+
+	while (sourceIndex < sourceLength) {
+		mergePtr->readID = sourcePtr->readID;
+		setShortReadMarkerPosition(mergePtr, -1);
+		setShortReadMarkerOffset(mergePtr, -1);
+		mergeLength++;
+		mergePtr++;
+		sourceIndex++;
+		sourcePtr++;
+	}
+
+	while (targetIndex < targetLength) {
+		mergePtr->readID = targetPtr->readID;
+		setShortReadMarkerPosition(mergePtr, targetPtr->position);
+		setShortReadMarkerOffset(mergePtr, targetPtr->offset);
+		mergeLength++;
+		mergePtr++;
+		targetIndex++;
+		targetPtr++;
+	}
+
+	free(targetArray);
+	graph->nodeReads[targetID] = mergeArray;
+	graph->nodeReadCounts[targetID] = mergeLength;
+}
+
+static inline Coordinate min(Coordinate A, Coordinate B)
+{
+	return A < B ? A : B;
+}
+
+static inline ShortLength min_short(ShortLength A, ShortLength B)
+{
+	return A < B ? A : B;
+}
+
+void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,
+		      Node * target, Graph * graph)
+{
+	IDnum targetID = getNodeID(target) + graph->nodeCount;
+	ShortReadMarker *targetArray = graph->nodeReads[targetID];
+	IDnum targetLength = graph->nodeReadCounts[targetID];
+	ShortReadMarker *targetPtr = targetArray;
+	ShortReadMarker *sourcePtr = sourceArray;
+	ShortReadMarker *mergeArray, *mergePtr;
+	IDnum mergeLength;
+	Coordinate targetPosition, sourcePosition;
+	ShortLength targetOffset, sourceOffset;
+	IDnum targetIndex, targetVal, sourceIndex, sourceVal;
+
+	if (sourceLength == 0) {
+		free(sourceArray);
+		return;
+	}
+
+	if (targetLength == 0) {
+		free(targetArray);
+		graph->nodeReads[targetID] = sourceArray;
+		graph->nodeReadCounts[targetID] = sourceLength;
+		return;
+	}
+
+	mergeArray =
+	    mallocOrExit(sourceLength +
+		    targetLength, ShortReadMarker);
+	mergePtr = mergeArray;
+
+	mergeLength = 0;
+	sourceIndex = 0;
+	targetIndex = 0;
+	targetVal = targetPtr->readID;
+	targetPosition = targetPtr->position;
+	targetOffset = targetPtr->offset;
+	sourceVal = sourcePtr->readID;
+	sourcePosition = sourcePtr->position;
+	sourceOffset = sourcePtr->offset;
+
+	while (sourceIndex < sourceLength && targetIndex < targetLength) {
+		if (sourceVal < targetVal) {
+			mergePtr->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr,
+						   sourcePosition);
+			setShortReadMarkerOffset(mergePtr, sourceOffset);
+			sourceIndex++;
+			if (sourceIndex < sourceLength) {
+				sourcePtr++;
+				sourceVal = sourcePtr->readID;
+				sourcePosition = sourcePtr->position;
+				sourceOffset = sourcePtr->offset;
+			}
+		} else if (sourceVal == targetVal) {
+			mergePtr->readID = sourceVal;
+			if (sourcePosition == -1 && targetPosition == -1) {
+				setShortReadMarkerPosition(mergePtr, -1);
+				setShortReadMarkerOffset(mergePtr, -1);
+			} else if (sourcePosition == -1) {
+				setShortReadMarkerPosition(mergePtr,
+							   targetPosition);
+				setShortReadMarkerOffset(mergePtr,
+							 targetOffset);
+			} else if (targetPosition == -1) {
+				setShortReadMarkerPosition(mergePtr,
+							   sourcePosition);
+				setShortReadMarkerOffset(mergePtr,
+							 sourceOffset);
+			} else {
+				setShortReadMarkerPosition(mergePtr,
+							   min
+							   (sourcePosition,
+							    targetPosition));
+				setShortReadMarkerOffset(mergePtr,
+							 min_short
+							 (sourceOffset,
+							  targetOffset));
+			}
+			sourceIndex++;
+			if (sourceIndex < sourceLength) {
+				sourcePtr++;
+				sourceVal = sourcePtr->readID;
+				sourcePosition = sourcePtr->position;
+				sourceOffset = sourcePtr->offset;
+			}
+			targetIndex++;
+			if (targetIndex < targetLength) {
+				targetPtr++;
+				targetVal = targetPtr->readID;
+				targetPosition = targetPtr->position;
+				targetOffset = targetPtr->offset;
+			}
+		} else {
+			mergePtr->readID = targetVal;
+			setShortReadMarkerPosition(mergePtr,
+						   targetPosition);
+			setShortReadMarkerOffset(mergePtr, targetOffset);
+			targetIndex++;
+			if (targetIndex < targetLength) {
+				targetPtr++;
+				targetVal = targetPtr->readID;
+				targetPosition = targetPtr->position;
+				targetOffset = targetPtr->offset;
+			}
+		}
+
+		mergeLength++;
+		mergePtr++;
+	}
+
+	while (sourceIndex < sourceLength) {
+		mergePtr->readID = sourcePtr->readID;
+		setShortReadMarkerPosition(mergePtr, sourcePtr->position);
+		setShortReadMarkerOffset(mergePtr, sourcePtr->offset);
+		mergeLength++;
+		mergePtr++;
+		sourceIndex++;
+		sourcePtr++;
+	}
+
+	while (targetIndex < targetLength) {
+		mergePtr->readID = targetPtr->readID;
+		setShortReadMarkerPosition(mergePtr, targetPtr->position);
+		setShortReadMarkerOffset(mergePtr, targetPtr->offset);
+		mergeLength++;
+		mergePtr++;
+		targetIndex++;
+		targetPtr++;
+	}
+
+	free(targetArray);
+	graph->nodeReads[targetID] = mergeArray;
+	graph->nodeReadCounts[targetID] = mergeLength;
+
+	free(sourceArray);
+}
+
+void mergeNodeReads(Node * target, Node * source, Graph * graph)
+{
+	IDnum sourceID, sourceLength;
+	ShortReadMarker *sourceArray;
+
+	if (graph->nodeReads == NULL || source == NULL || target == NULL)
+		return;
+
+	sourceID = getNodeID(source) + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+
+	if (sourceArray == NULL)
+		return;
+
+	graph->nodeReads[sourceID] = NULL;
+	graph->nodeReadCounts[sourceID] = 0;
+
+	injectShortReads(sourceArray, sourceLength, target, graph);
+}
+
+void foldSymmetricalNodeReads(Node * node, Graph * graph)
+{
+	IDnum targetID, targetLength, targetIndex;
+	IDnum sourceID, sourceLength, sourceIndex;
+	IDnum targetVal = 0;
+	IDnum sourceVal = 0;
+	IDnum mergeLength;
+	ShortReadMarker *sourceArray, *targetArray, *mergeArray,
+	    *mergeArray2;
+	ShortReadMarker *sourcePtr, *targetPtr, *mergePtr, *mergePtr2;
+
+	if (graph->nodeReads == NULL || node == NULL)
+		return;
+
+	sourceID = getNodeID(node) + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+	sourcePtr = sourceArray;
+
+	targetID = -getNodeID(node) + graph->nodeCount;
+	targetArray = graph->nodeReads[targetID];
+	targetLength = graph->nodeReadCounts[targetID];
+	targetPtr = targetArray;
+
+	if (sourceArray == NULL && targetArray == NULL)
+		return;
+
+	mergeArray =
+	    mallocOrExit(sourceLength +
+		    targetLength, ShortReadMarker);
+	mergeArray2 =
+	    mallocOrExit(sourceLength +
+		    targetLength, ShortReadMarker);
+	mergePtr = mergeArray;
+	mergePtr2 = mergeArray2;
+
+	mergeLength = 0;
+	sourceIndex = 0;
+	targetIndex = 0;
+	if (targetIndex < targetLength)
+		targetVal = targetPtr->readID;
+	if (sourceIndex < sourceLength)
+		sourceVal = sourcePtr->readID;
+
+	while (sourceIndex < sourceLength && targetIndex < targetLength) {
+		if (sourceVal < targetVal) {
+			mergePtr->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr2->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr2, -1);
+			setShortReadMarkerOffset(mergePtr2, -1);
+			sourceIndex++;
+			sourcePtr++;
+			if (sourceIndex < sourceLength)
+				sourceVal = sourcePtr->readID;
+		} else if (sourceVal == targetVal) {
+			mergePtr->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr2->readID = sourceVal;
+			setShortReadMarkerPosition(mergePtr2, -1);
+			setShortReadMarkerOffset(mergePtr2, -1);
+			sourceIndex++;
+			sourcePtr++;
+			if (sourceIndex < sourceLength)
+				sourceVal = sourcePtr->readID;
+			targetIndex++;
+			targetPtr++;
+			if (targetIndex < targetLength)
+				targetVal = targetPtr->readID;
+		} else {
+			mergePtr->readID = targetVal;
+			setShortReadMarkerPosition(mergePtr, -1);
+			setShortReadMarkerOffset(mergePtr, -1);
+			mergePtr2->readID = targetVal;
+			setShortReadMarkerPosition(mergePtr2, -1);
+			setShortReadMarkerOffset(mergePtr2, -1);
+			targetIndex++;
+			targetPtr++;
+			if (targetIndex < targetLength)
+				targetVal = targetPtr->readID;
+		}
+
+		mergeLength++;
+		mergePtr++;
+		mergePtr2++;
+	}
+
+	while (sourceIndex < sourceLength) {
+		mergePtr->readID = sourcePtr->readID;
+		setShortReadMarkerPosition(mergePtr, -1);
+		setShortReadMarkerOffset(mergePtr, -1);
+		mergePtr2->readID = sourcePtr->readID;
+		setShortReadMarkerPosition(mergePtr2, -1);
+		setShortReadMarkerOffset(mergePtr2, -1);
+		mergeLength++;
+		mergePtr++;
+		mergePtr2++;
+		sourceIndex++;
+		sourcePtr++;
+	}
+
+	while (targetIndex < targetLength) {
+		mergePtr->readID = targetPtr->readID;
+		setShortReadMarkerPosition(mergePtr, -1);
+		setShortReadMarkerOffset(mergePtr, -1);
+		mergePtr2->readID = targetPtr->readID;
+		setShortReadMarkerPosition(mergePtr2, -1);
+		setShortReadMarkerOffset(mergePtr2, -1);
+		mergeLength++;
+		mergePtr++;
+		mergePtr2++;
+		targetIndex++;
+		targetPtr++;
+	}
+
+	free(targetArray);
+	graph->nodeReads[targetID] = mergeArray;
+	graph->nodeReadCounts[targetID] = mergeLength;
+
+	free(sourceArray);
+	graph->nodeReads[sourceID] = mergeArray2;
+	graph->nodeReadCounts[sourceID] = mergeLength;
+}
+
+void shareReadStarts(Node * target, Node * source, Graph * graph)
+{
+	ShortReadMarker *sourceArray;
+	IDnum sourceLength, sourceID;
+
+	if (graph->nodeReads == NULL)
+		return;
+
+	if (target == NULL || source == NULL)
+		return;
+
+	sourceID = source->ID + graph->nodeCount;
+	sourceArray = graph->nodeReads[sourceID];
+	sourceLength = graph->nodeReadCounts[sourceID];
+
+	if (sourceArray == NULL)
+		return;
+
+	spreadReadIDs(sourceArray, sourceLength, target, graph);
+}
+
+ShortReadMarker **getNodeToReadMappings(Graph * graph)
+{
+	return graph->nodeReads;
+}
+
+IDnum getShortReadMarkerID(ShortReadMarker * marker)
+{
+	return marker->readID;
+}
+
+inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker)
+{
+	return marker->offset;
+}
+
+inline void setShortReadMarkerOffset(ShortReadMarker * marker,
+				     ShortLength offset)
+{
+	marker->offset = offset;
+}
+
+IDnum *getNodeReadCounts(Graph * graph)
+{
+	return graph->nodeReadCounts;
+}
+
+int getWordLength(Graph * graph)
+{
+	return graph->wordLength;
+}
+
+ShortReadMarker *getNodeReads(Node * node, Graph * graph)
+{
+	IDnum id = node->ID + graph->nodeCount;
+	return graph->nodeReads[id];
+}
+
+IDnum getNodeReadCount(Node * node, Graph * graph)
+{
+	IDnum id = node->ID + graph->nodeCount;
+	return graph->nodeReadCounts[id];
+}
+
+inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker)
+{
+	return marker->position;
+}
+
+inline void setShortReadMarkerPosition(ShortReadMarker * marker,
+				       Coordinate position)
+{
+	if (position < -100)
+		return;
+
+	marker->position = position;
+}
+
+ShortReadMarker *getShortReadMarkerAtIndex(ShortReadMarker * array,
+					   IDnum index)
+{
+	return &(array[index]);
+}
+
+void destroyGraph(Graph * graph)
+{
+	IDnum index;
+	Node *node;
+	for (index = 1; index <= graph->nodeCount; index++) {
+		node = getNodeInGraph(graph, index);
+		if (node != NULL)
+			destroyNode(node, graph);
+	}
+
+	if (graph->gapMarkers)
+		deactivateGapMarkers(graph);
+
+	free(graph->nodes);
+	destroyRecycleBin(nodeMemory);
+	destroyRecycleBin(arcMemory);
+	destroyAllPassageMarkers();
+	free(graph->arcLookupTable);
+	free(graph->nodeReads);
+	free(graph->nodeReadCounts);
+	free(graph);
+}
+
+void setInsertLengths(Graph * graph, Category cat, Coordinate insertLength,
+		      Coordinate insertLength_std_dev)
+{
+	graph->insertLengths[cat] = insertLength;
+	graph->insertLengths_var[cat] =
+	    insertLength_std_dev * insertLength_std_dev;
+}
+
+Coordinate getInsertLength(Graph * graph, Category cat)
+{
+	return graph->insertLengths[cat / 2];
+}
+
+double getInsertLength_var(Graph * graph, Category cat)
+{
+	return graph->insertLengths_var[cat / 2];
+}
+
+void activateGapMarkers(Graph * graph)
+{
+	graph->gapMarkers =
+	    callocOrExit(graph->nodeCount + 1, GapMarker *);
+	gapMarkerMemory = newRecycleBin(sizeof(GapMarker), GAPBLOCKSIZE);
+}
+
+void deactivateGapMarkers(Graph * graph)
+{
+	free(graph->gapMarkers);
+	graph->gapMarkers = NULL;
+	destroyRecycleBin(gapMarkerMemory);
+	gapMarkerMemory = NULL;
+}
+
+static GapMarker *allocateGapMarker()
+{
+	return (GapMarker *) allocatePointer(gapMarkerMemory);
+}
+
+void appendGap(Node * node, Coordinate length, Graph * graph)
+{
+	IDnum nodeID = getNodeID(node);
+	GapMarker *marker = allocateGapMarker();
+	GapMarker *tmp;
+
+	marker->length = length;
+
+	if (nodeID > 0) {
+		marker->position = node->length;
+		marker->next = graph->gapMarkers[nodeID];
+		graph->gapMarkers[nodeID] = marker;
+	} else {
+		for (tmp = graph->gapMarkers[-nodeID]; tmp != NULL;
+		     tmp = tmp->next)
+			tmp->position += length;
+
+		marker->position = 0;
+		marker->next = graph->gapMarkers[-nodeID];
+		graph->gapMarkers[-nodeID] = marker;
+	}
+
+	addBufferToDescriptor(node, length);
+}
+
+void appendNodeGaps(Node * destination, Node * source, Graph * graph)
+{
+	IDnum destinationID = getNodeID(destination);
+	IDnum sourceID = getNodeID(source);
+	GapMarker *marker;
+
+	if (graph->gapMarkers == NULL)
+		return;
+
+	if (destinationID > 0 && sourceID > 0) {
+		for (marker = graph->gapMarkers[sourceID]; marker != NULL;
+		     marker = marker->next)
+			marker->position += destination->length;
+	} else if (destinationID > 0 && sourceID < 0) {
+		sourceID = -sourceID;
+		for (marker = graph->gapMarkers[sourceID]; marker != NULL;
+		     marker = marker->next)
+			marker->position =
+			    source->length + destination->length -
+			    marker->position - marker->length;
+	} else if (destinationID < 0 && sourceID > 0) {
+		destinationID = -destinationID;
+		for (marker = graph->gapMarkers[destinationID];
+		     marker != NULL; marker = marker->next)
+			marker->position += source->length;
+
+		for (marker = graph->gapMarkers[sourceID]; marker != NULL;
+		     marker = marker->next)
+			marker->position =
+			    source->length - marker->position -
+			    marker->length;
+	} else {
+		destinationID = -destinationID;
+		sourceID = -sourceID;
+		for (marker = graph->gapMarkers[destinationID];
+		     marker != NULL; marker = marker->next)
+			marker->position += source->length;
+	}
+
+	if (graph->gapMarkers[destinationID] == NULL)
+		graph->gapMarkers[destinationID] =
+		    graph->gapMarkers[sourceID];
+	else {
+		marker = graph->gapMarkers[destinationID];
+		while (marker->next != NULL)
+			marker = marker->next;
+		marker->next = graph->gapMarkers[sourceID];
+	}
+
+	graph->gapMarkers[sourceID] = NULL;
+}
+
+GapMarker *getGap(Node * node, Graph * graph)
+{
+	IDnum nodeID = getNodeID(node);
+
+	if (graph->gapMarkers == NULL)
+		return NULL;
+
+	if (nodeID < 0)
+		nodeID = -nodeID;
+
+	return graph->gapMarkers[nodeID];
+}
+
+GapMarker *getNextGap(GapMarker * marker)
+{
+	return marker->next;
+}
+
+Coordinate getGapStart(GapMarker * marker)
+{
+	return marker->position;
+}
+
+Coordinate getGapFinish(GapMarker * marker)
+{
+	return marker->position + marker->length;
+}
+
+void reallocateNodeDescriptor(Node * node, Coordinate length) {
+	Coordinate arrayLength, index, shift;
+	Node * twin = node->twinNode;
+	Descriptor * array;
+	Nucleotide nucleotide;
+
+	if (length < node->length)
+		exitErrorf(EXIT_FAILURE, true, "Sum of node lengths smaller than first!");
+
+	shift = length - node->length;
+
+	arrayLength = length / 4;
+	if (length % 4)
+		arrayLength++;
+
+	node->descriptor = reallocOrExit(node->descriptor, arrayLength, Descriptor);
+
+	array = callocOrExit(arrayLength, Descriptor);
+	for (index = node->length - 1; index >= 0; index--) {
+		nucleotide = getNucleotideInDescriptor(twin->descriptor, index);
+		writeNucleotideInDescriptor(nucleotide, array, index + shift);
+	}
+	
+	free(twin->descriptor);
+	twin->descriptor = array;
+}
+
+boolean doubleStrandedGraph(Graph * graph) {
+	return graph->double_stranded;
+}