bio-velvet_underground 0.0.1

data/ext/src/src/graphReConstruction.h

@@ -0,0 +1,30 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#ifndef _GRAPHRECONSTRUCTION_H_
+#define _GRAPHRECONSTRUCTION_H_
+
+Graph *importPreGraph(char *preGraphFilename, ReadSet * reads, char * roadmapFilename, 
+		      boolean readTracking, short int accelerationBits);
+
+Graph *importConnectedGraph(char *connectedGraphFilename, ReadSet * reads, char * roadmapFilename, 
+		      boolean readTracking, short int accelerationBits);
+
+#endif

data/ext/src/src/graphStats.c

@@ -0,0 +1,2167 @@
+/*
+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 <math.h>
+#include <string.h>
+#include <ctype.h>
+
+#include "globals.h"
+#include "graph.h"
+#include "graphStats.h"
+#include "readSet.h"
+#include "tightString.h"
+#include "passageMarker.h"
+#include "concatenatedGraph.h"
+#include "readCoherentGraph.h"
+#include "fibHeap.h"
+#include "utility.h"
+#include "recycleBin.h"
+#include "passageMarker.h"
+#include "binarySequences.h"
+
+static PassageMarkerList *copyMarkers(Node * node)
+{
+	PassageMarkerList *list = NULL;
+	PassageMarkerList *new;
+	PassageMarkerI currentMarker;
+
+	for (currentMarker = getMarker(node); currentMarker != NULL_IDX;
+	     currentMarker = getNextInNode(currentMarker)) {
+		new = newPassageMarkerList(currentMarker, list);
+		list = new;
+	}
+
+	return list;
+}
+
+static boolean removeDead(PassageMarkerList ** list)
+{
+	PassageMarkerList *current, *next;
+	boolean removed = false;
+
+	if (*list == NULL)
+		return false;
+
+	current = *list;
+
+	while (current->next != NULL) {
+		next = current->next;
+
+		if (isTerminal(next->marker)) {
+			removed = true;
+			current->next = next->next;
+			deallocatePassageMarkerList(next);
+		} else
+			current = current->next;
+	}
+
+	current = *list;
+	if (isTerminal(current->marker)) {
+		removed = true;
+		*list = current->next;
+		deallocatePassageMarkerList(current);
+	}
+
+	return removed;
+}
+
+static Node *chooseDestination(PassageMarkerList * list)
+{
+	PassageMarkerList *current = list;
+	Node *destination;
+
+	destination = getNode(getNextInSequence(current->marker));
+	while (current != NULL) {
+		if (getNode(getNextInSequence(current->marker)) !=
+		    destination)
+			return NULL;
+		current = current->next;
+	}
+
+	return destination;
+}
+
+static void destroyPassageMarkerList(PassageMarkerList ** list)
+{
+	PassageMarkerList *ptr;
+
+	while (*list != NULL) {
+		ptr = *list;
+		*list = ptr->next;
+		deallocatePassageMarkerList(ptr);
+	}
+}
+
+static void updateMarkers(PassageMarkerList * list)
+{
+	PassageMarkerList *current;
+
+	for (current = list; current != NULL; current = current->next)
+		current->marker = getNextInSequence(current->marker);
+}
+
+Coordinate computeSubsequentNodesLength(Node * node)
+{
+	PassageMarkerList *list;
+	Node *nextNode;
+	Coordinate totalLength = 0;
+	boolean uncertain = false;
+
+	list = copyMarkers(node);
+
+	while (true) {
+		if (removeDead(&list))
+			uncertain = true;
+
+		if (uncertain && simpleArcCount(node) > 1) {
+			destroyPassageMarkerList(&list);
+			return totalLength;
+		}
+
+		if (list == NULL)
+			return totalLength;
+
+		nextNode = chooseDestination(list);
+		if (nextNode == NULL) {
+			destroyPassageMarkerList(&list);
+			return totalLength;
+		}
+
+		totalLength += getNodeLength(nextNode);
+
+		updateMarkers(list);
+	}
+
+	// Impossible instruction
+	return -1;
+}
+
+Coordinate computeVirtualNodeLength(Node * node)
+{
+	Coordinate virtualLength;
+
+	if (node == NULL)
+		return 0;
+
+	virtualLength = getNodeLength(node);
+
+	virtualLength += computeSubsequentNodesLength(node);
+	virtualLength += computeSubsequentNodesLength(getTwinNode(node));
+
+	return virtualLength;
+}
+
+// Counts the number of markers for one node
+int nodeGenomicMultiplicity(Node * node, IDnum firstStrain)
+{
+	int counter = 0;
+	PassageMarkerI marker;
+
+	if (node == NULL)
+		return 0;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			counter++;
+
+	return counter;
+}
+
+boolean isOnlyGenome(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) >= firstStrain)
+			return false;
+
+	return true;
+}
+
+boolean isOnlyStrain(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			return false;
+
+	return true;
+}
+
+boolean isSNP(Node * node, IDnum firstStrain, int WORDLENGTH)
+{
+	IDnum sequence;
+	Coordinate position;
+
+	if (getNodeLength(node) != WORDLENGTH)
+		return false;
+
+	if (getMarker(node) == NULL_IDX)
+		return false;
+
+	if (getAbsolutePassMarkerSeqID(getMarker(node)) >= firstStrain)
+		return false;
+
+	if (getNextInNode(getMarker(node)) != NULL_IDX)
+		return false;
+
+	if (arcCount(node) != 1)
+		return false;
+
+	if (arcCount(getTwinNode(node)) != 1)
+		return false;
+
+	if (isOnlyGenome(getDestination(getArc(node)), firstStrain))
+		return false;
+
+	if (isOnlyGenome
+	    (getDestination(getArc(getTwinNode(node))), firstStrain))
+		return false;
+
+	sequence = getPassageMarkerSequenceID(getMarker(node));
+
+	if (sequence >= 0)
+		position = getPassageMarkerStart(getMarker(node));
+	else {
+		sequence = -sequence;
+		position = getPassageMarkerFinish(getMarker(node));
+	}
+
+	velvetLog("SNP\t%lld\t%ld\n", (long long) position, (long) sequence);
+
+	return true;
+}
+
+void removeStrainMarkers(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+	PassageMarkerI tmp = NULL_IDX;
+
+	marker = getMarker(node);
+	while (marker != NULL_IDX) {
+		tmp = getNextInNode(marker);
+
+		if (getAbsolutePassMarkerSeqID(marker) >= firstStrain)
+			destroyPassageMarker(marker);
+		marker = tmp;
+	}
+
+}
+
+Coordinate commonLength(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker = getMarker(node);
+	int orig = 0;
+	int strain = 0;
+
+	while (marker != NULL_IDX) {
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			orig++;
+		else
+			strain++;
+		marker = getNextInNode(marker);
+	}
+
+	if (orig == 0 || strain == 0)
+		return 0;
+
+	return (Coordinate) orig *getNodeLength(node);
+}
+
+boolean isMixed(Node * node, IDnum firstStrain)
+{
+	return !isOnlyStrain(node, firstStrain)
+	    && !isOnlyGenome(node, firstStrain);
+}
+
+int countLocalBreakpoints(PassageMarkerI marker, IDnum firstStrain)
+{
+	PassageMarkerI localMarker;
+	IDnum sequenceID = getAbsolutePassMarkerSeqID(marker);
+	IDnum localSeqID;
+	Coordinate start = getPassageMarkerStart(marker);
+	Node *localNode = getNode(marker);
+	Node *destination;
+	Arc *arc;
+	int arcCount = 0;
+	int arcIndex;
+	boolean *arcStatus;
+	int counter = 0;
+
+	if (!isMixed(localNode, firstStrain))
+		return 0;
+
+	// Count arcs
+	for (arc = getArc(localNode); arc != NULL; arc = getNextArc(arc))
+		arcCount++;
+	arcStatus = callocOrExit(arcCount, boolean);
+	// Check for other genomic markers in node
+	for (localMarker = getMarker(localNode); localMarker != NULL_IDX;
+	     localMarker = getNextInNode(localMarker)) {
+		localSeqID = getAbsolutePassMarkerSeqID(localMarker);
+		if (localSeqID >= firstStrain)
+			continue;
+
+		if (localSeqID < sequenceID)
+			return 0;
+
+		if (localSeqID == sequenceID
+		    && getPassageMarkerStart(localMarker) < start)
+			return 0;
+
+		destination = getNode(getNextInSequence(localMarker));
+
+		// Enter into table:
+		arcIndex = 0;
+		for (arc = getArc(localNode);
+		     getDestination(arc) != destination;
+		     arc = getNextArc(arc))
+			arcIndex++;
+		arcStatus[arcIndex] = true;
+	}
+
+	// Check other nodes
+	arcIndex = 0;
+	for (arc = getArc(localNode); arc != NULL; arc = getNextArc(arc)) {
+		if (!arcStatus[arcIndex]
+		    && isMixed(getDestination(arc), firstStrain))
+			counter++;
+		arcIndex++;
+	}
+
+	free(arcStatus);
+	return counter;
+}
+
+IDnum genomeMarkerCount(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+	IDnum counter = 0;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			counter++;
+
+	return counter;
+}
+
+Coordinate readCoverage(Node * node)
+{
+	PassageMarkerI marker;
+	Coordinate sum = 0;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker)) {
+		if (getTwinMarker(marker) == NULL_IDX) {
+			velvetLog("Node %li screwed up\n", (long) getNodeID(node));
+			velvetLog("Sequence %li\n",
+			       (long) getPassageMarkerSequenceID(marker));
+			abort();
+		}
+		sum += getPassageMarkerLength(marker);
+	}
+
+	return sum;
+}
+
+Coordinate refReadCoverage(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+	Coordinate sum = 0;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			sum += getPassageMarkerLength(marker);
+
+	return sum;
+}
+
+Coordinate newReadCoverage(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+	Coordinate sum = 0;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) >= firstStrain) {
+			sum += getPassageMarkerLength(marker);
+			if (getPassageMarkerLength(marker) < 0)
+				velvetLog("Bizarre marker %li at node %li\n",
+				       (long) getPassageMarkerSequenceID(marker),
+				       (long) getNodeID(node));
+		}
+
+	return sum;
+}
+
+static void printShortCounts(FILE * outfile, Node * node, Graph * graph, ReadSet * reads)
+{
+	IDnum counts[CATEGORIES];
+	Category cat;
+	IDnum shortReadIndex;
+	IDnum readID;
+	IDnum shortReadCount;
+	ShortReadMarker *array;
+	ShortReadMarker *marker;
+
+	if (!readStartsAreActivated(graph)) {
+		for (cat = 0; cat < CATEGORIES; cat++)
+			velvetFprintf(outfile, "\tN/A");
+		return;
+	}
+
+	shortReadCount = getNodeReadCount(node, graph);
+	array = getNodeReads(node, graph);
+
+	for (cat = 0; cat < CATEGORIES; cat++)
+		counts[cat] = 0;
+
+	for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
+		marker = getShortReadMarkerAtIndex(array, shortReadIndex);
+		readID = getShortReadMarkerID(marker);
+		cat = reads->categories[readID - 1] / 2;
+		counts[cat]++;
+	}
+
+	for (cat = 0; cat < CATEGORIES; cat++)
+		velvetFprintf(outfile, "\t%li", (long) counts[cat]);
+}
+
+void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads)
+{
+	IDnum nodeIndex;
+	Node *node;
+	Category cat;
+	FILE *outfile;
+
+	outfile = fopen(filename, "w");
+	if (outfile == NULL) {
+		velvetLog("Couldn't open file %s, sorry\n", filename);
+		return;
+	} else
+		velvetLog("Writing into stats file %s...\n", filename);
+
+	velvetFprintf(outfile, "ID\tlgth\tout\tin\tlong_cov");
+
+#ifndef SINGLE_COV_CAT
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		velvetFprintf(outfile, "\tshort%i_cov", (int) (cat + 1));
+		velvetFprintf(outfile, "\tshort%i_Ocov", (int) (cat + 1));
+	}
+#else
+	velvetFprintf(outfile, "\tshort_cov");
+#endif
+
+	velvetFprintf(outfile, "\tlong_nb");
+	for (cat = 0; cat < CATEGORIES; cat++) {
+		velvetFprintf(outfile, "\tshort%i_nb", (int) (cat + 1));
+	}
+
+	velvetFprintf(outfile, "\n");
+
+	for (nodeIndex = 1; nodeIndex <= nodeCount(graph); nodeIndex++) {
+		node = getNodeInGraph(graph, nodeIndex);
+		if (node == NULL)
+			continue;
+		velvetFprintf
+		    (outfile, "%ld\t%lld\t%i\t%i",
+		     (long) getNodeID(node), (long long) getNodeLength(node), arcCount(node),
+		     arcCount(getTwinNode(node)));
+
+		if (getNodeLength(node) > 0) {
+			velvetFprintf(outfile, "\t%f",
+				readCoverage(node) /
+				(double) getNodeLength(node));
+#ifndef SINGLE_COV_CAT
+			for (cat = 0; cat < CATEGORIES; cat++) {
+				velvetFprintf(outfile, "\t%f",
+					getVirtualCoverage(node, cat) /
+					(double) getNodeLength(node));
+				velvetFprintf(outfile, "\t%f",
+					getOriginalVirtualCoverage(node, cat) /
+					(double) getNodeLength(node));
+			}
+#else
+			velvetFprintf(outfile, "\t%f",
+					getVirtualCoverage(node) /
+					(double) getNodeLength(node));
+#endif
+		} else {
+			velvetFprintf(outfile, "\tInf");
+#ifndef SINGLE_COV_CAT
+			for (cat = 0; cat < CATEGORIES; cat++)
+				velvetFprintf(outfile, "\tInf\tInf");
+#else
+			velvetFprintf(outfile, "\tInf");
+#endif
+		}
+
+		velvetFprintf(outfile, "\t%li", (long) markerCount(node));
+		printShortCounts(outfile, node, graph, reads); 
+
+		velvetFprintf(outfile, "\n");
+	}
+
+	fclose(outfile);
+}
+
+void displayLocalBreakpoint(PassageMarkerI strainMarker,
+			    IDnum firstStrain,
+			    PassageMarkerI genomeMarker,
+			    Node ** genomeDestination,
+			    Node ** strainDestination, IDnum * counter,
+			    IDnum nodeCount)
+{
+	boolean isTranslocation;
+	PassageMarkerI marker;
+	Node *destination, *destinationA;
+	Node *destination2, *destination2A;
+	Node *node1, *node2;
+	IDnum localID = getNodeID(getNode(strainMarker));
+
+	// Eliminate genomic markers
+	if (strainMarker == genomeMarker)
+		return;
+
+	destinationA = getNode(getNextInSequence(strainMarker));
+
+	if (destinationA == NULL)
+		return;
+
+	// Eliminate those that follow some local strain
+	if (isDestinationToMarker(genomeMarker, destinationA)) {
+//              velvetLog("Parallel paths\n");
+		return;
+	}
+
+	destination2A = getNode(getNextInSequence(genomeMarker));
+
+	if (destination2A == NULL)
+		return;
+
+	velvetLog("Lengths %lld %lld\n", (long long) getNodeLength(destinationA),
+	       (long long) getNodeLength(destination2A));
+
+	// Hop to another genomic node
+//      if (getNodeLength(destinationA) > 24) {
+	//velvetLog("wrong length %d %d\n", getNodeLength(destination) , getNodeID(destination));
+//              return;
+//      }
+
+	destination =
+	    getNode(getNextInSequence(getNextInSequence(strainMarker)));
+
+	if (destination == NULL)
+		return;
+
+	// Eliminate those that point to uniquely strain sequences 
+	if (nodeGenomicMultiplicity(destination, firstStrain) != 1) {
+//              velvetLog("Multiple genome reads\n");
+		return;
+	}
+	// Hop to another genomic node
+//      if (getNodeLength(destination2A) != 24) {
+	//velvetLog("wrong length 2\n");
+//              return;
+//      }
+
+	destination2 =
+	    getNode(getNextInSequence(getNextInSequence(genomeMarker)));
+
+	if (destination2 == NULL)
+		return;
+
+
+	if (destination == destination2)
+		return;
+
+	// Eliminate those that point to uniquely strain sequences 
+	if (isOnlyGenome(destination2, firstStrain))
+		return;
+
+	setSingleNodeStatus(getNode(strainMarker), true);
+	strainDestination[localID + nodeCount] = destination;
+	genomeDestination[localID + nodeCount] = destination2;
+
+//      velvetLog("Assigning %p and %p to %d\n", destination, destination2, localID);
+	velvetLog("lengths %lld\t%lld\n", (long long) getNodeLength(destinationA),
+	       (long long) getNodeLength(destination2A));
+
+	// Detect translocation
+	isTranslocation = true;
+	for (marker = getMarker(destination); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) ==
+		    getAbsolutePassMarkerSeqID(genomeMarker)) {
+			isTranslocation = false;
+			break;
+		}
+
+	if (isTranslocation) {
+		velvetLog("BREAK TRANS\t%ld\t%lld\t%lld\t%lld\n",
+		       (long) getAbsolutePassMarkerSeqID(genomeMarker),
+		       (long long) getPassageMarkerStart(genomeMarker),
+		       (long long) getNodeLength(destinationA),
+		       (long long) getNodeLength(destination2A));
+		counter[2]++;
+		return;
+	}
+	// Detect breakpoint
+	velvetLog("BREAK INTRA\t%ld\t%lld\t%lld\t%lld\n",
+	       (long) getAbsolutePassMarkerSeqID(genomeMarker),
+	       (long long) getPassageMarkerStart(genomeMarker),
+	       (long long) getNodeLength(destinationA), (long long) getNodeLength(destination2A));
+	counter[1]++;
+
+	// Check for inversion
+	if (getPassageMarkerSequenceID(marker) !=
+	    -getPassageMarkerSequenceID(genomeMarker))
+		return;
+
+//      velvetLog("potential!!\n");
+
+	node1 = getTwinNode(destination);
+
+	if (getNodeStatus(node1)) {
+		node2 =
+		    getTwinNode(genomeDestination
+				[getNodeID(node1) + nodeCount]);
+		if (getNodeStatus(node2))
+			if (strainDestination[getNodeID(node2) + nodeCount]
+			    == destination2) {
+//                                      velvetLog("Safe\n");
+				counter[1] -= 4;
+				counter[0]++;
+			} else;
+//                              velvetLog("stopped 3\n");
+		else;
+//                      velvetLog("stopped 2\n");
+	} else;
+//              velvetLog("stopped 1\n");
+}
+
+PassageMarkerI genomeMarker(Node * node, IDnum firstStrain)
+{
+	PassageMarkerI marker;
+
+	if (genomeMarkerCount(node, firstStrain) != 1)
+		return NULL_IDX;
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		if (getAbsolutePassMarkerSeqID(marker) < firstStrain)
+			return marker;
+
+	return NULL_IDX;
+}
+
+void exportArcSequence(Arc * arc, FILE * outfile, int WORDLENGTH,
+		       TightString ** sequences)
+{
+	char *str;
+	TightString *output =
+	    newTightString(getNodeLength(getOrigin(arc)) +
+			   getNodeLength(getDestination(arc)));
+	appendNodeSequence(getOrigin(arc), output, 0);
+	appendNodeSequence(getDestination(arc), output,
+			   getNodeLength(getOrigin(arc)));
+	str = readTightString(output);
+	velvetFprintf(outfile, "> ARC from NODE %li", (long) getNodeID(getOrigin(arc)));
+	velvetFprintf(outfile, "%s\n", str);
+	destroyTightString(output);
+	free(str);
+}
+
+// Produce sequences necessary to recreate graph elsewhere...
+void projectGraphToFile(Graph * graph, char *filename, int WORDLENGTH,
+			TightString ** sequences)
+{
+	FILE *outfile = fopen(filename, "w");
+	IDnum index;
+	Node *currentNode;
+	Arc *arc;
+
+	if (outfile == NULL) {
+		velvetLog("Could not open %s, sorry\n", filename);
+		return;
+	}
+
+	for (index = 1; index < nodeCount(graph); index++) {
+		currentNode = getNodeInGraph(graph, index);
+		for (arc = getArc(currentNode); arc != NULL;
+		     arc = getNextArc(arc))
+			exportArcSequence(arc, outfile, WORDLENGTH,
+					  sequences);
+
+		for (arc = getArc(getTwinNode(currentNode)); arc != NULL;
+		     arc = getNextArc(arc))
+			exportArcSequence(arc, outfile, WORDLENGTH,
+					  sequences);
+	}
+
+	fclose(outfile);
+}
+
+static RecycleBin * maskMemory = NULL;
+
+static Mask *allocateMask()
+{
+	if (maskMemory == NULL)
+		maskMemory = newRecycleBin(sizeof(Mask), 10000);
+
+	return (Mask *) allocatePointer(maskMemory);
+}
+
+static void deallocateMask(Mask * mask)
+{
+	deallocatePointer(maskMemory, mask);
+}
+
+
+static Mask * newMask(Coordinate position)
+{
+	Mask * mask = allocateMask();
+	mask->start = position;
+	mask->finish = position;
+	mask->next = NULL;
+	return mask;
+}
+
+static Mask * lowCoverageRegions(Coordinate * starts, Coordinate * stops, size_t length, IDnum cutoff, Coordinate nodeLength) {
+	size_t indexStart = 0;
+	size_t indexStop = 0;
+	int currentValue = 0;
+	Mask * regions = NULL;
+	Mask * lastRegion = NULL;
+	boolean openMask = false;
+
+	while (indexStart < length && indexStop < length) {
+		if (starts[indexStart] == stops[indexStop]) {
+			indexStart++;
+			indexStop++;
+		} else if (starts[indexStart] < stops[indexStop]) {
+			if (currentValue == cutoff - 1 && lastRegion) {
+				lastRegion->finish = starts[indexStart] - 1;
+				openMask = false;
+			}
+			currentValue++;
+			indexStart++;
+		} else {
+			if (currentValue == cutoff && stops[indexStop] != nodeLength) {
+				if (regions) {
+					lastRegion->next = newMask(stops[indexStop]);
+					lastRegion = lastRegion->next;
+				} else { 
+					regions = newMask(stops[indexStop]);
+					lastRegion = regions;
+				}
+				openMask = true;
+			}
+			currentValue--;
+			indexStop++;
+		}
+	}
+
+	while (indexStart < length) {
+		if (currentValue == cutoff - 1 && lastRegion) {
+			lastRegion->finish = starts[indexStart] - 1;
+			openMask = false;
+		} else if (currentValue >= cutoff) {
+			break;
+		}
+		currentValue++;
+		indexStart++;
+	}
+
+	while (indexStop < length) {
+		if (currentValue == cutoff + 1) {
+			if (regions) {
+				lastRegion->next = newMask(stops[indexStop]);
+				lastRegion = lastRegion->next;
+			} else { 
+				regions = newMask(stops[indexStop]);
+				lastRegion = regions;
+			}
+			openMask = true;
+		} else if (currentValue < cutoff)
+			break;
+		currentValue--;
+		indexStop++;
+	}
+
+	if (openMask)
+		lastRegion->finish = nodeLength;
+
+	free(starts);
+	free(stops);
+	return regions;
+}
+
+static int compareCoords(const void * A, const void * B) {
+	Coordinate * a_p = (Coordinate *) A;
+	Coordinate * b_p = (Coordinate *) B;
+	Coordinate a = * a_p;
+	Coordinate b = * b_p;
+	if (a < b)
+		return -1;
+	else if (a > b)
+		return 1;
+	else
+		return 0;
+}
+
+static void sortCoords(Coordinate * array, IDnum length) {
+	qsort(array, (size_t) length, sizeof(Coordinate), compareCoords);
+} 
+
+static void getShortReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths) {
+	ShortReadMarker * markers = getNodeReads(node, graph);
+	ShortReadMarker* marker;
+	IDnum index;
+	for (index = 0; index < getNodeReadCount(node, graph); index++) {
+		marker = getShortReadMarkerAtIndex(markers, index);
+		starts[index] = getShortReadMarkerPosition(marker);
+		stops[index] = starts[index] - getShortReadMarkerOffset(marker) + readLengths[getShortReadMarkerID(marker) - 1] - 1;
+	}
+}
+
+static void getShortReadTwinCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ShortLength * readLengths, IDnum offset) {
+	ShortReadMarker * markers = getNodeReads(getTwinNode(node), graph);
+	ShortReadMarker* marker;
+	IDnum index;
+	for (index = 0; index < getNodeReadCount(getTwinNode(node), graph); index++) {
+		marker = getShortReadMarkerAtIndex(markers, index);
+		stops[index + offset] = getNodeLength(node) - 1 - getShortReadMarkerPosition(marker);
+		starts[index + offset] = stops[index + offset] + getShortReadMarkerOffset(marker) - readLengths[getShortReadMarkerID(marker) - 1] + 1;
+	}
+}
+
+static void getLongReadCoords(Coordinate * starts, Coordinate * stops, Node * node, Graph * graph, ReadSet * reads, IDnum offset) {
+	PassageMarkerI marker;
+	IDnum index = offset;
+
+	for (marker = getMarker(node); marker; marker = getNextInNode(marker)) {
+		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] != REFERENCE) {
+			starts[index] = getStartOffset(marker);
+			stops[index++] = getNodeLength(node) - 1 - getFinishOffset(marker);
+		} else {
+			starts[index] = -5;
+			stops[index++] = -10;
+		}
+	}
+}
+
+static Mask * findLowCoverageRegions(Node * node, Graph * graph, IDnum cutoff, ReadSet * reads, ShortLength * readLengths) {
+	// Fill arrays
+	IDnum nodeReads = getNodeReadCount(node, graph);
+	IDnum twinReads =  getNodeReadCount(getTwinNode(node), graph);
+	IDnum longReads = markerCount(node);
+	IDnum length = nodeReads + twinReads + longReads;
+	Coordinate * starts = callocOrExit(length, Coordinate);
+	Coordinate * stops = callocOrExit(length, Coordinate);
+	getShortReadCoords(starts, stops, node, graph, readLengths);
+	getShortReadTwinCoords(starts, stops, node, graph, readLengths, nodeReads);
+	getLongReadCoords(starts, stops, node, graph, reads, nodeReads + twinReads);
+
+	// Sort arrays
+	sortCoords(starts, length);
+	sortCoords(stops, length);
+
+	// Go through array
+	return lowCoverageRegions(starts, stops, length, cutoff, getNodeLength(node));
+}
+
+static void exportLongNodeSequence(FILE * outfile, Node * node, Graph * graph, ReadSet * reads, ShortLength * readLengths, IDnum cutoff) {
+	TightString *tString;
+	Coordinate position;
+	char nucleotide;
+	int WORDLENGTH = getWordLength(graph);
+	GapMarker *gap;
+	IDnum nodeIndex = getNodeID(node);
+	Mask * mask = NULL;
+	Mask * next;
+
+	if (readStartsAreActivated(graph) && cutoff > 0)
+		mask = findLowCoverageRegions(node, graph, cutoff, reads, readLengths);
+
+	tString = expandNode(node, WORDLENGTH);
+	velvetFprintf(outfile, ">NODE_%ld_length_%lld_cov_%f\n",
+		(long) nodeIndex, (long long) getNodeLength(node),
+		(getTotalCoverage(node) + readCoverage(node)) /
+		(float) getNodeLength(node));
+
+	gap = getGap(node, graph);
+	for (position = 0; position < WORDLENGTH; position++) {
+		if (position % 60 == 0 && position > 0)
+			velvetFprintf(outfile, "\n"); 
+		nucleotide = getNucleotideChar(position, tString);
+		velvetFprintf(outfile, "%c", nucleotide);
+	}
+
+	gap = getGap(node, graph);
+	for (; position < getLength(tString); position++) {
+		if (position % 60 == 0)
+			velvetFprintf(outfile, "\n");
+
+		while (gap
+		    && position - WORDLENGTH + 1 >=
+		    getGapFinish(gap))
+			gap = getNextGap(gap);
+
+		while (mask
+		    && position - WORDLENGTH + 1 >=
+		    mask->finish) {
+			next = mask->next;
+			deallocateMask(mask);
+			mask = next;	
+		}
+
+		if (gap
+		    && position - WORDLENGTH + 1 >=
+		    getGapStart(gap)) {
+			velvetFprintf(outfile, "N");
+		} else if (mask &&
+			position - WORDLENGTH + 1 >=
+			mask->start) {
+			nucleotide =
+			    getNucleotideChar(position, tString);
+			velvetFprintf(outfile, "%c", tolower(nucleotide));
+
+		} else {
+			nucleotide =
+			    getNucleotideChar(position, tString);
+			velvetFprintf(outfile, "%c", nucleotide);
+		}
+	}
+	velvetFprintf(outfile, "\n");
+	destroyTightString (tString);
+}
+
+void exportLongNodeSequences(char *filename, Graph * graph,
+			     Coordinate minLength, ReadSet * reads, ShortLength * readLengths, IDnum minCov)
+{
+	FILE *outfile = fopen(filename, "w");
+	IDnum nodeIndex;
+	Node *node;
+	//double sensitivity, specificity;
+
+	if (outfile == NULL) {
+		velvetLog("Could not write into %s, sorry\n", filename);
+		return;
+	} else {
+		velvetLog("Writing contigs into %s...\n", filename);
+	}
+
+	for (nodeIndex = 1; nodeIndex <= nodeCount(graph); nodeIndex++) {
+		node = getNodeInGraph(graph, nodeIndex);
+
+		if (node == NULL || getNodeLength(node) < minLength)
+			continue;
+
+		exportLongNodeSequence(outfile, node, graph, reads, readLengths, minCov);
+	}
+
+	if (maskMemory)
+		destroyRecycleBin(maskMemory);
+	maskMemory = NULL;
+
+	fclose(outfile);
+}
+
+Coordinate maxLength(Graph * graph)
+{
+	IDnum index;
+	Node *node;
+	Coordinate max = 0;
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+		if (node != NULL && getNodeLength(node) > max)
+			max = getNodeLength(node);
+	}
+
+	return max;
+}
+
+Coordinate n50(Graph * graph)
+{
+	FibHeap *heap = newFibHeap();
+	IDnum index;
+	Coordinate totalLength = 0;
+	Coordinate sumLength = 0;
+	Node *node;
+
+	if (nodeCount(graph) == 0) {
+		velvetLog("EMPTY GRAPH\n");
+		return 0;
+	}
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+		if (node == NULL)
+			continue;
+		insertNodeIntoHeap(heap, getNodeLength(node), node);
+		totalLength += getNodeLength(node);
+	}
+	totalLength /= 2;
+
+	node = removeNextNodeFromHeap(heap);
+	while (node != NULL) {
+		sumLength += getNodeLength(node);
+		if (sumLength >= totalLength)
+			break;
+		node = removeNextNodeFromHeap(heap);
+	}
+
+	destroyHeap(heap);
+	return getNodeLength(node);
+}
+
+int compareNodeCovs(const void * A, const void * B) {
+	Node * nodeA = *((Node **) A);
+	Node * nodeB = *((Node **) B);
+	double covA;
+	double covB;
+	
+	if (getNodeLength(nodeA) == 0)
+		nodeA = NULL;
+
+	if (getNodeLength(nodeB) == 0)
+		nodeB = NULL;
+
+	// Null nodes considered to have infinite coverage
+	if (nodeA == NULL && nodeB == NULL)
+		return 0;
+	if (nodeA == NULL)
+		return 1;
+	if (nodeB == NULL)
+		return -1;
+
+	// Deal with real coverage numbers:
+	covA = getTotalCoverage(nodeA) / (double) getNodeLength(nodeA);	
+	covB = getTotalCoverage(nodeB) / (double) getNodeLength(nodeB);	
+
+	if (covA > covB)
+		return 1;
+	if (covA == covB)
+		return 0;
+	return -1;
+}
+
+double estimated_cov(Graph * graph, char * directory)
+{
+	Node ** nodeArray = callocOrExit(nodeCount(graph), Node*); 
+	IDnum index;
+	Coordinate halfTotalLength = 0;
+	Coordinate sumLength = 0;
+	Node *node;
+	char *logFilename =
+	    mallocOrExit(strlen(directory) + 100, char);
+	char *statsLine = 
+	    mallocOrExit(5000, char);
+	FILE *logFile;
+
+	strcpy(logFilename, directory);
+	strcat(logFilename, "/Log");
+	logFile = fopen(logFilename, "a");
+
+	if (logFile == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not write to %s",
+		       logFilename);
+
+	velvetLog("Measuring median coverage depth...\n");
+
+	if (nodeCount(graph) == 0) {
+		velvetLog("EMPTY GRAPH\n");
+		return 0;
+	}
+
+	// Write nodes into array and compute total assembly length
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+		nodeArray[index - 1] = node;
+		if (node == NULL)
+			continue;
+		halfTotalLength += getNodeLength(node);
+	}
+	halfTotalLength /= 2;
+
+	// Sort nodes
+	qsort(nodeArray, nodeCount(graph), sizeof(Node *), compareNodeCovs);
+
+	// Compute the length weighted median node coverage
+	for (index = 0; index < nodeCount(graph); index++) {
+		node = nodeArray[index];
+		sumLength += getNodeLength(node);
+		if (sumLength >= halfTotalLength) {
+			velvetLog("Median coverage depth = %f\n", getTotalCoverage(node) / (double) getNodeLength(node));
+			velvetFprintf(logFile, "Median coverage depth = %f\n", getTotalCoverage(node) / (double) getNodeLength(node));
+			free(nodeArray);
+			fclose(logFile);
+			free(logFilename);
+			free(statsLine);
+			return getTotalCoverage(node) / (double) getNodeLength(node);
+		}
+	}
+
+	// In case something went wrong...
+	free(nodeArray);
+	fclose(logFile);
+	free(logFilename);
+	free(statsLine);
+
+	return -1;
+}
+
+static boolean terminalReferenceMarker(Node * node, ReadSet * reads) {
+	PassageMarkerI marker;
+
+	for (marker = getMarker(node); marker; marker = getNextInNode(marker))
+		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] == REFERENCE
+		    && (!getNextInSequence(marker)
+		        || !getPreviousInSequence(marker)))
+			return true;
+
+	return false;
+}
+
+static boolean hasReferenceMarker(Node * node, ReadSet * reads) {
+	PassageMarkerI marker;
+	
+	for (marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker))
+		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] == REFERENCE)
+			return true;
+
+	return false;
+}
+
+inline static void
+destroyNodePassageMarkers(Graph *graph,
+			     Node* node)
+{
+	PassageMarkerI marker;
+
+	while ((marker = getMarker(node)) != NULL_IDX) {
+		if (!isInitial(marker) && !isTerminal(marker))
+			deleteNextPassageMarker(getPreviousInSequence(marker), graph);
+		destroyPassageMarker(marker);
+	}
+}
+
+inline static void
+removeNodeAndDenounceDubiousReads(Graph *graph,
+				  Node  *node,
+				  boolean denounceReads,
+				  boolean *res,
+				  Coordinate minLength,
+				  FILE *outfile)
+{
+	if (denounceReads) {
+		ShortReadMarker *nodeArray;
+		ShortReadMarker *shortMarker;
+		IDnum maxIndex;
+		IDnum index;
+		IDnum readID;
+
+		nodeArray = getNodeReads(node, graph);
+		maxIndex = getNodeReadCount(node, graph);
+		for (index = 0; index < maxIndex; index++) {
+			shortMarker = getShortReadMarkerAtIndex(nodeArray, index);
+			readID = getShortReadMarkerID(shortMarker);
+			if (readID > 0)
+				res[readID - 1] = true;
+			else
+				res[-readID - 1] = true;
+		}
+
+		nodeArray = getNodeReads(getTwinNode(node), graph);
+		maxIndex = getNodeReadCount(getTwinNode(node), graph);
+		for (index = 0; index < maxIndex; index++) {
+			shortMarker = getShortReadMarkerAtIndex(nodeArray, index);
+			readID = getShortReadMarkerID(shortMarker);
+			if (readID > 0)
+				res[readID - 1] = true;
+			else
+				res[-readID - 1] = true;
+		}
+	}
+
+	destroyNodePassageMarkers(graph, node);
+
+	if (outfile != NULL && getNodeLength(node) > minLength)
+		exportLongNodeSequence(outfile, node, graph, NULL, NULL, -1);
+
+	destroyNode(node, graph);
+}
+
+boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
+						       double minCov,
+						       ReadSet * reads,
+						       boolean export,
+						       Coordinate minLength,
+						       char *filename)
+{
+	IDnum index;
+	Node *node;
+	boolean denounceReads = readStartsAreActivated(graph);
+	boolean *res = NULL; 
+	FILE * outfile = NULL;
+
+	velvetLog("Removing contigs with coverage < %f...\n", minCov);
+		
+	if (denounceReads)
+		res = callocOrExit(sequenceCount(graph), boolean);
+		
+	if (export) {
+		outfile = fopen(filename, "w");
+
+		if (outfile == NULL) {
+			velvetLog("Could not write into %s, sorry\n", filename);
+			return res;
+		} else {
+			velvetLog("Writing contigs into %s...\n", filename);
+		}
+	}
+
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) == 0)
+			continue;
+
+		if (getTotalCoverage(node) / getNodeLength(node) < minCov 
+		    && !hasReferenceMarker(node, reads))
+			removeNodeAndDenounceDubiousReads(graph,
+							  node,
+							  denounceReads,
+							  res,
+							  minLength,
+							  outfile);
+	}
+
+	concatenateGraph(graph);
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) == 0)
+			continue;
+
+		if (getTotalCoverage(node) / getNodeLength(node) < minCov 
+		    && !terminalReferenceMarker(node, reads))
+			removeNodeAndDenounceDubiousReads(graph,
+							  node,
+							  denounceReads,
+							  res,
+							  minLength,
+							  outfile);
+	}
+
+	if (export)
+		fclose(outfile);
+
+	concatenateGraph(graph);
+	return res;
+}
+
+static Coordinate getLongCoverage(Node * node) {
+	PassageMarkerI marker;
+	Coordinate total = 0;
+
+	for (marker = getMarker(node); marker; marker = getNextInNode(marker))
+		total += getPassageMarkerLength(marker);
+	
+	return total;
+}
+
+void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLongCov, ReadSet * reads)
+{
+	IDnum index;
+	Node *node;
+
+	velvetLog("Removing reference contigs with coverage < %f...\n", minCov);
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) == 0)
+			continue;
+
+		if ((getTotalCoverage(node) / getNodeLength(node) < minCov 
+		    || getLongCoverage(node) / getNodeLength(node) < minLongCov)
+		    && hasReferenceMarker(node, reads)) {
+			destroyNodePassageMarkers(graph, node);
+
+			destroyNode(node, graph);
+		}
+	}
+
+	concatenateGraph(graph);
+}
+
+void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
+						       double minCov,
+						       ReadSet * reads,
+						       boolean * res,
+						       boolean export,
+						       Coordinate minLength,
+						       char *filename)
+{
+	IDnum index;
+	Node *node;
+	boolean denounceReads = readStartsAreActivated(graph);
+	FILE * outfile = NULL;
+
+	if (minCov < 0)
+		return;
+
+	velvetLog("Removing contigs with coverage < %f...\n", minCov);
+		
+	if (export) {
+		outfile = fopen(filename, "a");
+
+		if (outfile == NULL) {
+			velvetLog("Could not write into %s, sorry\n", filename);
+			return;
+		} else {
+			velvetLog("Writing contigs into %s...\n", filename);
+		}
+	}
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) == 0)
+			continue;
+
+		if (getLongCoverage(node) / getNodeLength(node) < minCov 
+		    && !hasReferenceMarker(node, reads))
+			removeNodeAndDenounceDubiousReads(graph,
+							  node,
+							  denounceReads,
+							  res,
+							  minLength,
+							  outfile);
+	}
+
+	concatenateGraph(graph);
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) == 0)
+			continue;
+
+		if (getLongCoverage(node) / getNodeLength(node) < minCov 
+		    && !terminalReferenceMarker(node, reads))
+			removeNodeAndDenounceDubiousReads(graph,
+							  node,
+							  denounceReads,
+							  res,
+							  minLength,
+							  outfile);
+	}
+
+	if (export)
+		fclose(outfile);
+
+	concatenateGraph(graph);
+}
+
+void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, char *filename)
+{
+	IDnum index;
+	Node *node;
+	FILE * outfile = NULL;
+
+	if (maxCov < 0)
+		return;
+
+	velvetLog("Applying an upper coverage cutoff of %f...\n", maxCov);
+		
+	if (export) {
+		outfile = fopen(filename, "w");
+
+		if (outfile == NULL) {
+			velvetLog("Could not write into %s, sorry\n", filename);
+			return;
+		} else {
+			velvetLog("Writing contigs into %s...\n", filename);
+		}
+	}
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (getNodeLength(node) > 0
+		    && getTotalCoverage(node) / getNodeLength(node) > maxCov) {
+			destroyNodePassageMarkers(graph, node);
+
+			if (export && getNodeLength(node) > minLength) 
+				exportLongNodeSequence(outfile, node, graph, NULL, NULL, -1);
+
+			destroyNode(node, graph);
+		}
+	}
+
+	if (export)
+		fclose(outfile);
+
+	concatenateGraph(graph);
+}
+
+static void exportAMOSLib(FILE * outfile, Graph * graph, Category cat)
+{
+	Coordinate distance = getInsertLength(graph, cat * 2);
+	double variance = getInsertLength_var(graph, cat * 2);
+
+	if (distance == -1)
+		return;
+
+	velvetFprintf(outfile, "{LIB\n");
+	velvetFprintf(outfile, "iid:%d\n", (int) (cat + 1));
+	velvetFprintf(outfile, "{DST\n");
+	velvetFprintf(outfile, "mea:%lld\n", (long long) distance);
+	velvetFprintf(outfile, "std:%lld\n", (long long) sqrt(variance));
+	velvetFprintf(outfile, "}\n");
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSMarker(FILE * outfile, PassageMarkerI marker,
+			     Coordinate nodeLength, Coordinate start,
+			     Coordinate finish, int wordShift)
+{
+	Coordinate sequenceStart, sequenceFinish;
+
+	if (getStartOffset(marker) >= finish
+	    || getFinishOffset(marker) > nodeLength - start)
+		return;
+
+	sequenceStart = getPassageMarkerStart(marker);
+	if (start > getStartOffset(marker)) {
+		if (getPassageMarkerSequenceID(marker) > 0)
+			sequenceStart += start - getStartOffset(marker);
+		else
+			sequenceStart -= start - getStartOffset(marker);
+	}
+
+	sequenceFinish = getPassageMarkerFinish(marker);
+	if (nodeLength - finish > getFinishOffset(marker)) {
+		if (getPassageMarkerSequenceID(marker) > 0)
+			sequenceFinish -=
+			    nodeLength - finish - getFinishOffset(marker);
+		else
+			sequenceFinish +=
+			    nodeLength - finish - getFinishOffset(marker);
+	}
+
+	if (getPassageMarkerSequenceID(marker) > 0)
+		sequenceFinish += wordShift;
+	else
+		sequenceStart += wordShift;
+
+	velvetFprintf(outfile, "{TLE\n");
+	velvetFprintf(outfile, "src:%li\n", (long) getAbsolutePassMarkerSeqID(marker));
+	if (getStartOffset(marker) > start)
+		velvetFprintf(outfile, "off:%lld\n",
+			(long long) (getStartOffset(marker) - start));
+	else
+		velvetFprintf(outfile, "off:0\n");
+	velvetFprintf(outfile, "clr:%lld,%lld\n", (long long) sequenceStart, (long long) sequenceFinish);
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSShortMarker(FILE * outfile, ShortReadMarker * marker,
+				  ReadSet * reads, Coordinate start,
+				  Coordinate finish)
+{
+	Coordinate offset =
+	    getShortReadMarkerPosition(marker) -
+	    getShortReadMarkerOffset(marker);
+	TightString *sequence =
+	    getTightStringInArray (reads->tSequences, getShortReadMarkerID(marker) - 1);
+
+	if (getShortReadMarkerPosition(marker) == -1)
+		return;
+
+	if (offset >= finish || offset + getLength(sequence) < start)
+		return;
+
+	velvetFprintf(outfile, "{TLE\n");
+	velvetFprintf(outfile, "src:%li\n", (long) getShortReadMarkerID(marker));
+	velvetFprintf(outfile, "off:%lld\n", (long long) (offset - start));
+	velvetFprintf(outfile, "clr:0,%lld\n", (long long) getLength(sequence));
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSReverseShortMarker(FILE * outfile,
+					 ShortReadMarker * marker,
+					 Coordinate nodeLength,
+					 int wordShift, ReadSet * reads,
+					 Coordinate start,
+					 Coordinate finish)
+{
+	TightString *sequence =
+	    getTightStringInArray (reads->tSequences, getShortReadMarkerID(marker) - 1);
+
+	Coordinate offset =
+	    nodeLength - getShortReadMarkerPosition(marker) +
+	    getShortReadMarkerOffset(marker) - getLength(sequence) +
+	    wordShift;
+
+	if (getShortReadMarkerPosition(marker) == -1)
+		return;
+
+	if (offset >= finish || offset + getLength(sequence) < start)
+		return;
+
+	velvetFprintf(outfile, "{TLE\n");
+	velvetFprintf(outfile, "src:%li\n", (long) getShortReadMarkerID(marker));
+	velvetFprintf(outfile, "off:%lld\n", (long long) (offset - start));
+	velvetFprintf(outfile, "clr:%lld,0\n", (long long) getLength(sequence));
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSContig(FILE * outfile, ReadSet * reads, Node * node,
+			     Graph * graph, Coordinate contigStart,
+			     Coordinate contigFinish, IDnum iid,
+			     IDnum internalIndex)
+{
+	Coordinate start;
+	char str[100];
+	PassageMarkerI marker;
+	ShortReadMarker *shortMarkerArray, *shortMarker;
+	Coordinate index, maxIndex;
+	int wordShift = getWordLength(graph) - 1;
+	char *string = expandNodeFragment(node, contigStart, contigFinish,
+					  getWordLength(graph));
+	Coordinate length = contigFinish - contigStart + wordShift;
+
+	velvetFprintf(outfile, "{CTG\n");
+	velvetFprintf(outfile, "iid:%li\n", (long) iid);
+	velvetFprintf(outfile, "eid:%li-%li\n", (long) getNodeID(node), (long) internalIndex);
+
+	velvetFprintf(outfile, "seq:\n");
+	for (start = 0; start <= length; start += 60) {
+		strncpy(str, &(string[start]), 60);
+		str[60] = '\0';
+		velvetFprintf(outfile, "%s\n", str);
+	}
+	velvetFprintf(outfile, ".\n");
+
+	velvetFprintf(outfile, "qlt:\n");
+	for (start = 0; start <= length; start += 60) {
+		strncpy(str, &(string[start]), 60);
+		str[60] = '\0';
+		velvetFprintf(outfile, "%s\n", str);
+	}
+	velvetFprintf(outfile, ".\n");
+
+	free(string);
+
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		exportAMOSMarker(outfile, marker, getNodeLength(node),
+				 contigStart, contigFinish, wordShift);
+
+	if (readStartsAreActivated(graph)) {
+		shortMarkerArray = getNodeReads(node, graph);
+		maxIndex = getNodeReadCount(node, graph);
+		for (index = 0; index < maxIndex; index++) {
+			shortMarker =
+			    getShortReadMarkerAtIndex(shortMarkerArray,
+						      index);
+			exportAMOSShortMarker(outfile, shortMarker, reads,
+					      contigStart, contigFinish);
+		}
+
+		shortMarkerArray = getNodeReads(getTwinNode(node), graph);
+		maxIndex = getNodeReadCount(getTwinNode(node), graph);
+		for (index = 0; index < maxIndex; index++) {
+			shortMarker =
+			    getShortReadMarkerAtIndex(shortMarkerArray,
+						      index);
+			exportAMOSReverseShortMarker(outfile, shortMarker,
+						     getNodeLength(node),
+						     wordShift, reads,
+						     contigStart,
+						     contigFinish);
+		}
+	}
+
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSNode(FILE * outfile, ReadSet * reads, Node * node,
+			   Graph * graph)
+{
+	Coordinate start = 0;
+	Coordinate finish;
+	GapMarker *gap;
+	IDnum smallIndex = 0;
+	static IDnum iid = 1;
+	IDnum contigIndex = iid;
+	int wordShift = getWordLength(graph) - 1;
+
+	for (gap = getGap(node, graph); gap; gap = getNextGap(gap)) {
+		finish = getGapStart(gap);
+		exportAMOSContig(outfile, reads, node, graph, start,
+				 finish, iid++, smallIndex++);
+		start = getGapFinish(gap);
+	}
+
+	finish = getNodeLength(node);
+	exportAMOSContig(outfile, reads, node, graph, start, finish, iid++,
+			 smallIndex);
+
+	if (!getGap(node, graph))
+		return;
+
+	start = 0;
+
+	velvetFprintf(outfile, "{SCF\n");
+	velvetFprintf(outfile, "eid:%li\n", (long) getNodeID(node));
+	for (gap = getGap(node, graph); gap; gap = getNextGap(gap)) {
+		finish = getGapStart(gap);
+		velvetFprintf(outfile, "{TLE\n");
+		velvetFprintf(outfile, "off:%lld\n", (long long) start);
+		velvetFprintf(outfile, "clr:0,%lld\n",
+			(long long) (finish - start + (long long) wordShift));
+		velvetFprintf(outfile, "src:%li\n", (long) contigIndex++);
+		velvetFprintf(outfile, "}\n");
+		start = getGapFinish(gap);
+	}
+	finish = getNodeLength(node);
+	velvetFprintf(outfile, "{TLE\n");
+	velvetFprintf(outfile, "off:%lld\n", (long long) start);
+	velvetFprintf(outfile, "clr:0,%lld\n", (long long) (finish - start));
+	velvetFprintf(outfile, "src:%li\n", (long) contigIndex++);
+	velvetFprintf(outfile, "}\n");
+
+	velvetFprintf(outfile, "}\n");
+}
+
+static void exportAMOSRead(FILE * outfile, TightString * tString,
+			   IDnum index, IDnum frg_index)
+{
+	Coordinate start, finish;
+	char str[100];
+
+	velvetFprintf(outfile, "{RED\n");
+	velvetFprintf(outfile, "iid:%li\n", (long) index);
+	velvetFprintf(outfile, "eid:%li\n", (long) index);
+	if (frg_index > 0)
+		velvetFprintf(outfile, "frg:%li\n", (long) frg_index);
+
+	velvetFprintf(outfile, "seq:\n");
+	start = 0;
+	while (start <= getLength(tString)) {
+		finish = start + 60;
+		readTightStringFragment(tString, start, finish, str);
+		velvetFprintf(outfile, "%s\n", str);
+		start = finish;
+	}
+	velvetFprintf(outfile, ".\n");
+
+	velvetFprintf(outfile, "qlt:\n");
+	start = 0;
+	while (start <= getLength(tString)) {
+		finish = start + 60;
+		readTightStringFragment(tString, start, finish, str);
+		velvetFprintf(outfile, "%s\n", str);
+		start = finish;
+	}
+	velvetFprintf(outfile, ".\n");
+
+	velvetFprintf(outfile, "}\n");
+}
+
+void exportAMOSContigs(char *filename, Graph * graph,
+		       Coordinate cutoff_length, ReadSet * reads)
+{
+	IDnum index;
+	Category cat;
+	Node *node;
+	FILE *outfile;
+
+	velvetLog("Writing into AMOS file %s...\n", filename);
+	outfile = fopen(filename, "w");
+
+	if (outfile == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not write to AMOS file %s",
+		       filename);
+
+	for (cat = 0; cat <= CATEGORIES; cat++)
+		exportAMOSLib(outfile, graph, cat);
+
+	for (index = 1; index <= reads->readCount; index++) {
+		if (reads->categories[index - 1] % 2 != 0 &&
+		    getInsertLength(graph,
+				    reads->categories[index - 1]) >= 0) {
+			velvetFprintf(outfile, "{FRG\n");
+			velvetFprintf(outfile, "lib:%d\n",
+				(int) ((reads->categories[index - 1] / 2) + 1));
+			velvetFprintf(outfile, "rds:%li,%li\n", (long) index,
+				(long) index + 1);
+			velvetFprintf(outfile, "eid:%li\n", (long) index);
+			velvetFprintf(outfile, "iid:%li\n", (long) index);
+			velvetFprintf(outfile, "typ:I\n");
+			velvetFprintf(outfile, "}\n");
+			index++;
+		}
+	}
+
+	for (index = 1; index <= reads->readCount; index++) {
+		if (reads->categories[index - 1] % 2 != 0 &&
+		    getInsertLength(graph,
+				    reads->categories[index - 1]) >= 0) {
+			exportAMOSRead(outfile,
+				       getTightStringInArray(reads->tSequences, index - 1), index,
+				       index);
+			index++;
+			exportAMOSRead(outfile,
+				       getTightStringInArray(reads->tSequences, index - 1), index,
+				       index - 1);
+		} else {
+			exportAMOSRead(outfile,
+				       getTightStringInArray(reads->tSequences, index - 1), index,
+				       -1);
+		}
+	}
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+
+		if (node == NULL)
+			continue;
+
+		if (getNodeLength(node) >= cutoff_length)
+			exportAMOSNode(outfile, reads, node, graph);
+	}
+
+	fclose(outfile);
+
+}
+
+Coordinate totalAssemblyLength(Graph * graph)
+{
+	IDnum index;
+	Node *node;
+	Coordinate total = 0;
+
+	for (index = 1; index <= nodeCount(graph); index++) {
+		node = getNodeInGraph(graph, index);
+		if (node)
+			total += getNodeLength(node);
+	}
+
+	return total;
+}
+
+IDnum usedReads(Graph * graph, Coordinate minContigLength) 
+{
+	IDnum res = 0;
+	boolean * used = callocOrExit(sequenceCount(graph) + 1, boolean);
+	IDnum nodeID, readID;
+	Node * node;
+	PassageMarkerI marker;
+	ShortReadMarker * shortReadArray, * shortReadMarker;
+	IDnum shortReadCount, shortReadIndex;
+
+	for(nodeID = 1; nodeID <= nodeCount(graph); nodeID++) {
+		node = getNodeInGraph(graph, nodeID);
+		if (node == NULL || getNodeLength(node) < minContigLength)
+			continue;
+		
+		// Long reads
+		for(marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker)) {
+			readID = getPassageMarkerSequenceID(marker);
+			if (readID < 0)
+				readID = -readID;
+			used[readID] = true;	
+		}	
+
+		// Short reads		
+		if (!readStartsAreActivated(graph))
+			continue;
+
+		shortReadArray = getNodeReads(node, graph);
+		shortReadCount = getNodeReadCount(node, graph);
+		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
+			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
+			readID = getShortReadMarkerID(shortReadMarker);
+			used[readID] = true;	
+		}
+		
+		shortReadArray = getNodeReads(getTwinNode(node), graph);
+		shortReadCount = getNodeReadCount(getTwinNode(node), graph);
+		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
+			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
+			readID = getShortReadMarkerID(shortReadMarker);
+			used[readID] = true;	
+		}
+	}
+
+	for (readID = 1; readID <= sequenceCount(graph); readID++) 
+		if (used[readID])
+			res++;
+
+	free(used);	
+
+	return res;
+}
+
+void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *directory)
+{
+	char *logFilename =
+	    mallocOrExit(strlen(directory) + 100, char);
+	char *statsLine = 
+	    mallocOrExit(5000, char);
+	FILE *logFile;
+
+	strcpy(logFilename, directory);
+	strcat(logFilename, "/Log");
+	logFile = fopen(logFilename, "a");
+
+	if (logFile == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not write to %s",
+		       logFilename);
+
+	sprintf
+	    (statsLine, "Final graph has %ld nodes and n50 of %lld, max %lld, total %lld, using %ld/%ld reads\n",
+	     (long) nodeCount(graph), (long long) n50(graph), (long long) maxLength(graph),
+	     (long long) totalAssemblyLength(graph), (long) usedReads(graph, minContigKmerLength),
+	     (long) sequenceCount(graph));
+
+	velvetFprintf(logFile, "%s", statsLine);
+	velvetFprintf(stdout, "%s", statsLine);
+
+	fclose(logFile);
+	free(logFilename);
+	free(statsLine);
+}
+
+void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLength, char* directory) {
+	char *outFilename =
+	    mallocOrExit(strlen(directory) + 100, char);
+	FILE * outfile;
+	boolean * used = callocOrExit(sequenceCount(graph) + 1, boolean);
+	IDnum nodeID, readID;
+	Node * node;
+	PassageMarkerI marker;
+	ShortReadMarker * shortReadArray, * shortReadMarker;
+	IDnum shortReadCount, shortReadIndex;
+
+	strcpy(outFilename, directory);
+	strcat(outFilename, "/UnusedReads.fa");
+	outfile = fopen(outFilename, "w");
+
+	velvetLog("Printing unused reads into %s\n", outFilename);
+
+	for(nodeID = 1; nodeID <= nodeCount(graph); nodeID++) {
+		node = getNodeInGraph(graph, nodeID);
+		if (node == NULL || getNodeLength(node) < minContigKmerLength)
+			continue;
+		
+		// Long reads
+		for(marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker)) {
+			readID = getPassageMarkerSequenceID(marker);
+			if (readID < 0)
+				readID = -readID;
+			used[readID] = true;	
+		}	
+
+		// Short reads		
+		if (!readStartsAreActivated(graph))
+			continue;
+
+		shortReadArray = getNodeReads(node, graph);
+		shortReadCount = getNodeReadCount(node, graph);
+		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
+			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
+			readID = getShortReadMarkerID(shortReadMarker);
+			used[readID] = true;	
+		}
+		
+		shortReadArray = getNodeReads(getTwinNode(node), graph);
+		shortReadCount = getNodeReadCount(getTwinNode(node), graph);
+		for (shortReadIndex = 0; shortReadIndex < shortReadCount; shortReadIndex++) {
+			shortReadMarker = getShortReadMarkerAtIndex(shortReadArray, shortReadIndex);
+			readID = getShortReadMarkerID(shortReadMarker);
+			used[readID] = true;	
+		}
+	}
+
+	for (readID = 1; readID <= sequenceCount(graph); readID++) 
+		if (!used[readID])
+			exportTightString(outfile, getTightStringInArray(reads->tSequences, readID - 1), readID);
+
+	free(outFilename);
+	free(used);	
+	fclose(outfile);
+}
+
+static IDnum getReferenceCount(ReadSet * reads) {
+	IDnum index;
+
+	for (index = 0; index < reads->readCount; index++) 
+		if (reads->categories[index] != REFERENCE)
+			break;
+
+	return index;
+}
+
+//////////////////////////////////////////////////////////////////////////
+// Reference identifiers
+//////////////////////////////////////////////////////////////////////////
+
+typedef struct referenceCoord_st ReferenceCoord;
+
+struct referenceCoord_st {
+	IDnum start;
+	IDnum finish;
+	char * name;
+	boolean positive_strand;
+} ATTRIBUTE_PACKED;
+
+static ReferenceCoord * collectReferenceCoords(SequencesReader *seqReadInfo, IDnum referenceCount) {
+	ReferenceCoord * refCoords = callocOrExit(referenceCount, ReferenceCoord);
+	IDnum refIndex = 0;
+	if (seqReadInfo->m_bIsBinary) {
+	    velvetLog("Creating placeholder reference headers\n");
+	    // binary seqs does not have reference header so a placeholder is created
+	    do {
+		refCoords[refIndex].name = callocOrExit(sizeof("PLACEHLDR.%ld PLACEHOLDER000") + 20, char);
+		sprintf(refCoords[refIndex].name, "PLACEHLDR.%ld PLACEHOLDER000", (int64_t) refIndex + 1);
+		refCoords[refIndex].start = 1;
+		refCoords[refIndex].finish = -1;
+		refCoords[refIndex].positive_strand = true;
+	    } while (++refIndex < referenceCount);
+	} else {
+	    FILE * file = fopen(seqReadInfo->m_seqFilename, "r");
+	char line[MAXLINE];
+	char name[5000];
+	Coordinate start, finish;
+	long long longlongvar;
+	int i;
+
+	while (fgets(line, MAXLINE, file)) {
+		if (line[0] == '>') {
+			if (strchr(line, ':')) {
+				sscanf(strtok(line, ":-\r\n"), ">%s", name);
+				sscanf(strtok(NULL, ":-\r\n"), "%lli", &longlongvar);
+				start = longlongvar;
+				sscanf(strtok(NULL, ":-\r\n"), "%lli", &longlongvar);
+				finish = longlongvar;
+				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);  
+				if (start <= finish) {
+					strcpy(refCoords[refIndex].name, name);
+					refCoords[refIndex].start = start;
+					refCoords[refIndex].finish = finish;
+					refCoords[refIndex].positive_strand = true;
+				} else {
+					strcpy(refCoords[refIndex].name, name);
+					refCoords[refIndex].start = finish;
+					refCoords[refIndex].finish = start;
+					refCoords[refIndex].positive_strand = false;
+				}
+			} else {
+				for (i = strlen(line) - 1;
+				     i >= 0 && (line[i] == '\n' || line[i] == '\r'); i--) {
+					line[i] = '\0';
+				}
+
+				strcpy(name, line + 1);
+				refCoords[refIndex].name = callocOrExit(strlen(name) + 1, char);  
+				strcpy(refCoords[refIndex].name, name);
+				refCoords[refIndex].start = 1;
+				refCoords[refIndex].finish = -1;
+				refCoords[refIndex].positive_strand = true;
+			}
+			if (++refIndex == referenceCount)
+				break;	
+		}
+	}
+	
+	fclose(file);
+	}
+	return refCoords;
+}
+
+typedef struct refMap_st {
+	IDnum start;
+	IDnum finish;
+	IDnum refID;
+	IDnum refStart;
+	IDnum refFinish;
+} ATTRIBUTE_PACKED ReferenceMapping; 
+
+static int compareReferenceMappings(const void * A, const void * B) {
+	ReferenceMapping * refMapA = (ReferenceMapping *) A;
+	ReferenceMapping * refMapB = (ReferenceMapping *) B;
+	
+	if (refMapA->start < refMapB->start)
+		return -1;
+	else if (refMapA->start == refMapB->start)
+		return 0;
+	else 
+		return 1;
+}
+
+static void initializeReferenceMapping(ReferenceMapping * refMap, PassageMarkerI marker, Node * node) {
+	refMap->start = getStartOffset(marker);
+	refMap->finish = getNodeLength(node) - getFinishOffset(marker); 
+	refMap->refID = getPassageMarkerSequenceID(marker);
+	refMap->refStart = getPassageMarkerStart(marker);
+	refMap->refFinish = getPassageMarkerFinish(marker);
+}
+
+static void velvetFprintfReferenceMapping(FILE * file, ReferenceMapping * mapping, ReferenceCoord * refCoords, int wordLength) {
+	ReferenceCoord * refCoord;
+	Coordinate start, finish;
+
+	if (mapping->refID > 0) 
+		refCoord = &refCoords[mapping->refID - 1];
+	else
+		refCoord = &refCoords[-mapping->refID - 1];
+
+	if (mapping->refID > 0) {
+		if (refCoord->positive_strand) {
+			start = refCoord->start + mapping->refStart;
+			finish = refCoord->start + mapping->refFinish + wordLength - 2;
+		} else {
+			start = refCoord->finish - mapping->refStart + wordLength - 1;
+			finish = refCoord->finish - mapping->refFinish + 1;
+		}
+	} else {
+		if (refCoord->positive_strand) {
+			start = refCoord->start + mapping->refStart + wordLength - 1;
+			finish = refCoord->start + mapping->refFinish + 1;
+		} else {
+			start = refCoord->finish - mapping->refStart; 
+			finish = refCoord->finish - mapping->refFinish + wordLength;  
+		}
+	}
+		
+	velvetFprintf(file, "%lli\t%lli\t%s\t%lli\t%lli\n",
+		(long long) mapping->start + 1, (long long) mapping->finish + wordLength - 1, 
+		refCoord->name, (long long) start, (long long) finish);
+}
+
+static void exportLongNodeMapping(FILE * outfile, Node * node, ReadSet * reads, ReferenceCoord * refCoords, int wordLength) {
+	PassageMarkerI marker;
+	ReferenceMapping * referenceMappings;
+	IDnum index;
+	IDnum referenceCount = 0;
+
+	// Count reference sequences
+	for (marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker))
+		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] == REFERENCE)
+			referenceCount++;
+
+	// Header
+	velvetFprintf(outfile, ">contig_%li\n", (long) getNodeID(node));
+
+	// Create table
+	referenceMappings = callocOrExit(referenceCount, ReferenceMapping);	
+
+	// Initialize table
+	referenceCount = 0;
+	for (marker = getMarker(node); marker != NULL_IDX; marker = getNextInNode(marker))
+		if (reads->categories[getAbsolutePassMarkerSeqID(marker) - 1] == REFERENCE)
+			initializeReferenceMapping(&referenceMappings[referenceCount++], marker, node);
+
+	// Sort table
+	qsort(referenceMappings, referenceCount, sizeof(ReferenceMapping), compareReferenceMappings);
+
+	// Print table
+	for (index = 0; index < referenceCount; index++)
+		velvetFprintfReferenceMapping(outfile, &referenceMappings[index], refCoords, wordLength);
+
+	// Clean table
+	free(referenceMappings);
+}
+
+void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,
+			     Coordinate minLength, SequencesReader *seqReadInfo)
+{
+	FILE * outfile;
+	IDnum nodeIndex, refIndex;
+	Node *node;
+	ReferenceCoord * refCoords;
+	IDnum referenceCount = getReferenceCount(reads); 
+
+	if (referenceCount == 0)	
+		return;
+
+	refCoords = collectReferenceCoords(seqReadInfo, referenceCount);
+
+	outfile = fopen(filename, "w");
+	if (outfile == NULL) {
+		velvetLog("Could not write into %s, sorry\n", filename);
+		return;
+	} else {
+		velvetLog("Writing contigs into %s...\n", filename);
+	}
+
+	for (nodeIndex = 1; nodeIndex <= nodeCount(graph); nodeIndex++) {
+		node = getNodeInGraph(graph, nodeIndex);
+
+		if (node == NULL || getNodeLength(node) < minLength)
+			continue;
+		
+		exportLongNodeMapping(outfile, node, reads, refCoords, getWordLength(graph));
+	}
+
+	for (refIndex = 0; refIndex < referenceCount; refIndex++)
+		free(refCoords[refIndex].name);
+	free(refCoords);
+	fclose(outfile);
+}
+
+static void removeLowArcsFromNode(Node* node, Graph * graph, double cutoff) {
+	Arc * arc, * next;
+	if (node == NULL)
+		return;
+
+	for (arc = getArc(node); arc; arc = next) {
+		next = getNextArc(arc);
+		if (getMultiplicity(arc) <= cutoff)
+			destroyArc(arc, graph);
+	}
+}
+
+void removeLowArcs(Graph * graph, double cutoff) {
+	velvetLog("Removing single arcs\n");
+	IDnum index;
+	for (index = -nodeCount(graph); index <= nodeCount(graph); index++)
+		removeLowArcsFromNode(getNodeInGraph(graph, index), graph, cutoff);
+
+	concatenateGraph(graph);
+}