bio-velvet_underground 0.0.1

data/ext/src/src/scaffold.h

@@ -0,0 +1,64 @@
+/*
+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 _SSCAFFOLD_H_
+#define _SCAFFOLD_H_
+
+typedef struct connection_st Connection;
+
+//General scaffold function
+void buildScaffold(Graph * graph,
+		   ReadSet * reads,
+		   boolean * dubious,
+		   boolean * shadows);
+Connection *createNewConnection(IDnum nodeID, IDnum node2ID,
+				       IDnum direct_count,
+				       IDnum paired_count,
+				       Coordinate distance,
+				       double variance);
+void readjustConnection(Connection * connect, Coordinate distance,
+			       double variance, IDnum direct_count,
+			       IDnum paired_count);
+void destroyConnection(Connection * connect, IDnum nodeID);
+
+void cleanScaffoldMemory();
+
+void setUnreliableConnectionCutoff(int val);
+void setPairedExpFraction(double x);
+
+// Connection handlers
+Connection * getConnection(Node * node);
+
+Node * getConnectionDestination(Connection * connect);
+Coordinate getConnectionDistance(Connection * connect);
+Connection * getNextConnection(Connection * connect);
+Connection * getTwinConnection(Connection * connect);
+double getConnectionVariance(Connection * connect);
+IDnum getConnectionDirectCount(Connection * connect);
+IDnum getConnectionPairedCount(Connection * connect);
+
+void incrementConnectionDistance(Connection * connect, Coordinate increment);
+void printConnections(ReadSet * reads, boolean * shadows);
+void printScaffold(Graph * graph,
+		   ReadSet * reads,
+		   boolean * dubious,
+		   boolean * shadows);
+
+#endif

data/ext/src/src/shortReadPairs.c

@@ -0,0 +1,1243 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#include <stdlib.h>
+#include <stdio.h>
+#include <time.h>
+#include <math.h>
+
+#include "globals.h"
+#include "graph.h"
+#include "concatenatedGraph.h"
+#include "recycleBin.h"
+#include "locallyCorrectedGraph.h"
+#include "passageMarker.h"
+#include "readSet.h"
+#include "utility.h"
+#include "scaffold.h"
+
+#define BLOCK_SIZE  100000
+#define LN2 1.4
+#define BACKTRACK_CUTOFF 100
+
+typedef struct miniConnection_st MiniConnection;
+
+struct miniConnection_st {
+	Connection *frontReference;
+	Connection *backReference;
+	NodeList *nodeList;
+	float variance;
+	IDnum distance;
+}  ATTRIBUTE_PACKED;
+
+// Global pointers
+static Graph *graph;
+static NodeList *markedNodes;
+static RecycleBin *nodeListMemory = NULL;
+static MiniConnection *localScaffold = NULL;
+
+static NodeList *allocateNodeList()
+{
+	if (nodeListMemory == NULL)
+		nodeListMemory =
+		    newRecycleBin(sizeof(NodeList), BLOCK_SIZE);
+
+	return allocatePointer(nodeListMemory);
+}
+
+static void deallocateNodeList(NodeList * nodeList)
+{
+	deallocatePointer(nodeListMemory, nodeList);
+}
+
+static NodeList *recordNode(Node * node)
+{
+	NodeList *nodeList = allocateNodeList();
+	nodeList->node = node;
+	nodeList->next = markedNodes;
+	nodeList->previous = NULL;
+
+	if (markedNodes != NULL)
+		markedNodes->previous = nodeList;
+
+	markedNodes = nodeList;
+
+	return nodeList;
+}
+
+static void destroyNodeList(NodeList * nodeList)
+{
+	//velvetLog("Destroy NL  %p > %p > %p\n", nodeList->previous, nodeList, nodeList->next);
+
+	if (nodeList->previous != NULL)
+		nodeList->previous->next = nodeList->next;
+	else
+		markedNodes = nodeList->next;
+
+	if (nodeList->next != NULL)
+		nodeList->next->previous = nodeList->previous;
+
+	nodeList->previous = nodeList->next = NULL;
+
+	deallocateNodeList(nodeList);
+}
+
+static Node *popNodeRecord()
+{
+	MiniConnection *localConnect;
+
+	NodeList *nodeList = markedNodes;
+	Node *node;
+
+	if (markedNodes == NULL)
+		return NULL;
+
+	node = nodeList->node;
+	markedNodes = nodeList->next;
+	if (markedNodes != NULL)
+		markedNodes->previous = NULL;
+
+	localConnect =
+	    &localScaffold[getNodeID(nodeList->node) + nodeCount(graph)];
+	localConnect->nodeList = NULL;
+
+	deallocateNodeList(nodeList);
+	return node;
+}
+
+static void resetMiniConnection(Node * node, MiniConnection * localConnect,
+				Coordinate distance, double variance,
+				Connection * frontReference,
+				Connection * backReference, boolean status)
+{
+	setSingleNodeStatus(node, status);
+	localConnect->distance = distance;
+	localConnect->variance = variance;
+	localConnect->frontReference = frontReference;
+	localConnect->backReference = backReference;
+	localConnect->nodeList = recordNode(node);
+}
+
+static void setEmptyMiniConnection(Node * node)
+{
+	MiniConnection *localConnect =
+	    &localScaffold[getNodeID(node) + nodeCount(graph)];
+	localConnect->distance = 0;
+	localConnect->variance = 1;
+	localConnect->frontReference = NULL;
+	localConnect->backReference = NULL;
+	localConnect->nodeList = recordNode(node);
+	setSingleNodeStatus(node, true);
+}
+
+static void readjustMiniConnection(Node * node,
+				   MiniConnection * localConnect,
+				   Coordinate distance,
+				   Coordinate min_distance,
+				   double variance,
+				   Connection * frontReference,
+				   Connection * backReference)
+{
+
+	localConnect->distance =
+	    (variance * localConnect->distance +
+	     distance * localConnect->variance) / (variance +
+						   localConnect->variance);
+	localConnect->variance =
+	    (variance *
+	     localConnect->variance) / (variance + localConnect->variance);
+
+	if (frontReference != NULL)
+		localConnect->frontReference = frontReference;
+	if (backReference != NULL)
+		localConnect->backReference = backReference;
+
+	if (localConnect->distance > min_distance)
+		setSingleNodeStatus(node, 1);
+	else
+		setSingleNodeStatus(node, -1);
+}
+
+static void integrateDerivativeDistances(Connection * connect,
+					 Coordinate min_distance,
+					 boolean direction)
+{
+	Node *reference = getConnectionDestination(connect);
+	Node *destination;
+	IDnum destinationID;
+	Coordinate distance, baseDistance;
+	double variance, baseVariance;
+	Connection *connect2;
+	MiniConnection *localConnect;
+
+	// debug 
+	IDnum counter = 0;
+
+	if (!getUniqueness(reference))
+		return;
+
+	//velvetLog("Opposite node %li length %li at %li ± %f\n", getNodeID(reference), getNodeLength(reference), getConnectionDistance(connect), getConnectionVariance(connect));
+
+	baseDistance = getConnectionDistance(connect);
+	baseVariance = getConnectionVariance(connect);
+
+	for (connect2 = getConnection(reference);
+	     connect2 != NULL; connect2 = getNextConnection(connect2)) {
+		// Avoid null derivative
+		if (connect2 == getTwinConnection(connect))
+			continue;
+
+		destination = getConnectionDestination(connect2);
+
+		// Beware of directionality
+		if (!direction)
+			destination = getTwinNode(destination);
+
+		// Derivate values
+		destinationID = getNodeID(destination);
+		// Beware of directionality (bis)
+		if (direction)
+			distance = baseDistance - getConnectionDistance(connect2);
+		else
+			distance = getConnectionDistance(connect2) - baseDistance;
+		variance = getConnectionVariance(connect2) + baseVariance;
+		localConnect =
+		    &localScaffold[destinationID + nodeCount(graph)];
+
+		// Avoid over-projection
+		if (distance < min_distance) {
+			//velvetLog("Node %li not at distance %li± %f (min %li)\n", destinationID, distance, variance, min_distance);
+			continue;
+		}
+
+		counter++;
+
+		if (getNodeStatus(destination)) {
+			readjustMiniConnection(destination, localConnect,
+					       distance, min_distance,
+					       variance, NULL, NULL);
+		} else
+			resetMiniConnection(destination, localConnect,
+					    distance, variance, NULL, NULL,
+					    true);
+
+		//velvetLog("Node %li now at distance %li\n", destinationID, localConnect->distance);
+	}
+
+	//velvetLog("%li secondary distances added\n", counter);
+}
+
+static void markInterestingNodes(Node * node)
+{
+	Connection *connect;
+	Node *destination;
+	MiniConnection *localConnect;
+	Coordinate min_distance =
+	    getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
+
+	// Mark own node
+	setEmptyMiniConnection(node);
+
+	// Loop thru primary scaffold
+	for (connect = getConnection(node); connect != NULL;
+	     connect = getNextConnection(connect)) {
+		destination = getTwinNode(getConnectionDestination(connect));
+
+		localConnect =
+		    &localScaffold[getNodeID(destination) +
+				   nodeCount(graph)];
+
+		if (getNodeStatus(destination)) {
+			readjustMiniConnection(destination, localConnect,
+					       getConnectionDistance(connect),
+					       min_distance,
+					       getConnectionVariance(connect), connect,
+					       NULL);
+			localConnect->backReference = NULL;
+		} else {
+			resetMiniConnection(destination, localConnect,
+					    getConnectionDistance(connect),
+					    getConnectionVariance(connect), connect,
+					    NULL, true);
+		}
+
+		integrateDerivativeDistances(connect, min_distance, true);
+	}
+
+	// Loop thru twin's primary scaffold
+	for (connect = getConnection(getTwinNode(node)); connect != NULL;
+	     connect = getNextConnection(connect)) {
+		destination = getConnectionDestination(connect);
+		localConnect =
+		    &localScaffold[getNodeID(destination) +
+				   nodeCount(graph)];
+
+		if (getNodeStatus(destination))
+			readjustMiniConnection(destination, localConnect,
+					       -getConnectionDistance(connect),
+					       min_distance,
+					       getConnectionVariance(connect), NULL,
+					       connect);
+		else
+			resetMiniConnection(destination, localConnect,
+					    -getConnectionDistance(connect),
+					    getConnectionVariance(connect), NULL,
+					    connect, -1);
+
+		integrateDerivativeDistances(connect, min_distance, false);
+	}
+}
+
+void unmarkNode(Node * node, MiniConnection * localConnect)
+{
+	if (localConnect->frontReference != NULL
+	    || localConnect->backReference != NULL) {
+		if (getNodeStatus(node) > 0)
+			setSingleNodeStatus(node, 10);
+		else
+			setSingleNodeStatus(node, -10);
+	} else {
+		setSingleNodeStatus(node, false);
+		destroyNodeList(localConnect->nodeList);
+		localConnect->frontReference = NULL;
+		localConnect->backReference = NULL;
+		localConnect->nodeList = NULL;
+	}
+}
+
+void handicapNode(Node * node)
+{
+	if (getNodeStatus(node) > 0)
+		setSingleNodeStatus(node, 10);
+	else
+		setSingleNodeStatus(node, -10);
+}
+
+static void absorbExtension(Node * node, Node * extension)
+{
+	Arc *arc;
+
+	appendNodeGaps(node, extension, graph);
+	appendDescriptors(node, extension);
+
+	// Destroy old nodes    
+	while (getArc(node) != NULL)
+		destroyArc(getArc(node), graph);
+
+	// Create new
+	for (arc = getArc(extension); arc != NULL; arc = getNextArc(arc))
+		createAnalogousArc(node, getDestination(arc), arc, graph);
+}
+
+NodeList *getMarkedNodeList()
+{
+	return markedNodes;
+}
+
+static void absorbExtensionInScaffold(Node * node, Node * source)
+{
+	IDnum nodeID = getNodeID(node);
+	IDnum sourceID = getNodeID(source);
+	IDnum sourceIndex = sourceID + nodeCount(graph);
+	Node *twinSource = getTwinNode(source);
+	IDnum twinSourceIndex = getNodeID(twinSource) + nodeCount(graph);
+	Connection *connect, *original;
+	Node *destination;
+	IDnum destinationID;
+	Coordinate distance_shift =
+	    (getNodeLength(node) - getNodeLength(source)) / 2;
+	Coordinate min_distance =
+	    getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
+	MiniConnection *localConnect;
+	Coordinate distance;
+	double variance;
+	IDnum direct_count;
+	IDnum paired_count;
+
+	while ((connect = getConnection(source))) {
+		destination = getTwinNode(getConnectionDestination(connect));
+
+		if (destination == getTwinNode(node)) {
+			localConnect = &localScaffold[twinSourceIndex];
+			localConnect->frontReference = NULL;
+			unmarkNode(twinSource, localConnect);
+			destroyConnection(connect, sourceID);
+			continue;
+		}
+		if (destination == node) {
+			localConnect = &localScaffold[sourceIndex];
+			localConnect->backReference = NULL;
+			unmarkNode(source, localConnect);
+			destroyConnection(connect, sourceID);
+			continue;
+		}
+
+		destinationID = getNodeID(destination);
+		localConnect =
+		    &localScaffold[destinationID + nodeCount(graph)];
+		incrementConnectionDistance(connect, distance_shift);
+		distance = getConnectionDistance(connect);
+		variance = getConnectionVariance(connect);
+		direct_count = getConnectionDirectCount(connect);
+		paired_count = getConnectionPairedCount(connect);
+
+		if (getNodeStatus(destination)) {
+			readjustMiniConnection(destination, localConnect,
+					       distance, min_distance,
+					       variance, NULL, NULL);
+			if ((original = localConnect->frontReference))
+				readjustConnection(original, distance,
+						   variance, direct_count,
+						   paired_count);
+			else
+				localConnect->frontReference =
+				    createNewConnection(nodeID,
+							-destinationID,
+							direct_count,
+							paired_count,
+							distance,
+							variance);
+		} else
+			resetMiniConnection(destination, localConnect,
+					    distance, variance,
+					    createNewConnection(nodeID,
+								-destinationID,
+								direct_count,
+								paired_count,
+								distance,
+								variance),
+					    NULL, true);
+
+		integrateDerivativeDistances(connect, min_distance, true);
+
+		destroyConnection(connect, sourceID);
+	}
+
+	// Loop thru twin's primary scaffold
+	while ((connect = getConnection(getTwinNode(source)))) {
+		destination = getConnectionDestination(connect);
+
+		if (destination == node) {
+			localConnect = &localScaffold[sourceIndex];
+			localConnect->frontReference = NULL;
+			unmarkNode(source, localConnect);
+			destroyConnection(connect, -sourceID);
+			continue;
+		}
+		if (destination == getTwinNode(node)) {
+			localConnect = &localScaffold[twinSourceIndex];
+			localConnect->backReference = NULL;
+			unmarkNode(twinSource, localConnect);
+			destroyConnection(connect, -sourceID);
+			continue;
+		}
+
+		destinationID = getNodeID(destination);
+
+		localConnect =
+		    &localScaffold[destinationID + nodeCount(graph)];
+		incrementConnectionDistance(connect, -distance_shift);
+		distance = getConnectionDistance(connect);
+		variance = getConnectionVariance(connect);
+		direct_count = getConnectionDirectCount(connect);
+		paired_count = getConnectionPairedCount(connect);
+
+		if (distance > min_distance && getNodeStatus(destination) < 0) {
+			readjustMiniConnection(destination, localConnect,
+					       -distance, min_distance,
+					       variance, NULL, NULL);
+			if ((original = localConnect->backReference))
+				readjustConnection(original, distance,
+						   variance, direct_count,
+						   paired_count);
+		} else if (getNodeStatus(destination) < 0) {
+			if ((original = localConnect->backReference)) {
+				destroyConnection(original, -nodeID);
+				localConnect->backReference = NULL;
+			}
+			unmarkNode(destination, localConnect);
+		} else if (getNodeStatus(destination) > 0) {
+			if ((original = localConnect->frontReference)) {
+				destroyConnection(original, nodeID);
+				localConnect->frontReference = NULL;
+			}
+			unmarkNode(destination, localConnect);
+		} else if (distance > min_distance) {
+			resetMiniConnection(destination, localConnect,
+					    -distance, variance, NULL,
+					    createNewConnection(-nodeID,
+								destinationID,
+								direct_count,
+								paired_count,
+								distance,
+								variance),
+					    -1);
+			integrateDerivativeDistances(connect, min_distance, true);
+		}
+
+		destroyConnection(connect, -sourceID);
+	}
+}
+
+static void recenterNode(Node * node, Coordinate oldLength)
+{
+	IDnum nodeID = getNodeID(node);
+	Connection *connect, *next;
+	Coordinate distance_shift = (getNodeLength(node) - oldLength) / 2;
+	Coordinate min_distance =
+	    getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
+	MiniConnection *localConnect;
+
+	//velvetLog("Recentering node\n");
+
+	for (connect = getConnection(node); connect != NULL;
+	     connect = next) {
+		next = getNextConnection(connect);
+		incrementConnectionDistance(connect, -distance_shift);
+
+		if (getConnectionDistance(connect) < min_distance) {
+			//velvetLog("Unrecording %li\n",
+			//       -getNodeID(getConnectionDestination(connect)));
+			localConnect =
+			    &localScaffold[-getNodeID(getConnectionDestination(connect))
+					   + nodeCount(graph)];
+			localConnect->frontReference = NULL;
+			unmarkNode(getTwinNode(getConnectionDestination(connect)),
+				   localConnect);
+			destroyConnection(connect, nodeID);
+		} else if (getTwinConnection(connect) != NULL)
+			incrementConnectionDistance(getTwinConnection(connect), -distance_shift);
+	}
+
+	for (connect = getConnection(getTwinNode(node)); connect != NULL;
+	     connect = next) {
+		next = getNextConnection(connect);
+		incrementConnectionDistance(connect, distance_shift);
+
+		if (getTwinConnection(connect) != NULL)
+			incrementConnectionDistance(getTwinConnection(connect), distance_shift);
+	}
+}
+
+static void recenterLocalScaffold(Node * node, Coordinate oldLength)
+{
+	MiniConnection *localConnect;
+	Coordinate distance_shift = (getNodeLength(node) - oldLength) / 2;
+	Coordinate min_distance =
+	    getNodeLength(node) / 2 - BACKTRACK_CUTOFF;
+	NodeList *nodeList, *next;
+	IDnum node2ID;
+	Node *node2;
+
+	for (nodeList = markedNodes; nodeList != NULL; nodeList = next) {
+		next = nodeList->next;
+
+		node2 = nodeList->node;
+
+		if (node2 == node) {
+			setSingleNodeStatus(node2, 1);
+			continue;
+		}
+
+		node2ID = getNodeID(node2);
+		localConnect = &localScaffold[node2ID + nodeCount(graph)];
+		localConnect->distance -= distance_shift;
+
+		if (localConnect->distance < min_distance
+		    && localConnect->backReference == NULL
+		    && localConnect->frontReference == NULL)
+			unmarkNode(node2, localConnect);
+		else if (getNodeStatus(node2) > 0)
+			setSingleNodeStatus(node2, 1);
+		else if (getNodeStatus(node2) < 0)
+			setSingleNodeStatus(node2, -1);
+	}
+}
+
+static void adjustShortReads(Node * target, Node * source)
+{
+	ShortReadMarker *targetArray, *marker;
+	IDnum targetLength, index;
+	Coordinate position, nodeLength;
+
+	if (!readStartsAreActivated(graph))
+		return;
+
+	targetArray = getNodeReads(getTwinNode(target), graph);
+	targetLength = getNodeReadCount(getTwinNode(target), graph);
+
+	nodeLength = getNodeLength(source);
+
+	for (index = 0; index < targetLength; index++) {
+		marker = getShortReadMarkerAtIndex(targetArray, index);
+		position = getShortReadMarkerPosition(marker);
+		if (position != -1) {
+			position += nodeLength;
+			setShortReadMarkerPosition(marker, position);
+		}
+	}
+}
+
+static void adjustLongReads(Node * target, Coordinate nodeLength)
+{
+	PassageMarkerI marker;
+
+	for (marker = getMarker(target); marker != NULL_IDX;
+	     marker = getNextInNode(marker))
+		incrementFinishOffset(marker, nodeLength);
+}
+
+static boolean goesToNode(PassageMarkerI marker, Node * node)
+{
+	PassageMarkerI current;
+	Node * start = getNode(marker);
+
+	for (current = getNextInSequence(marker); current != NULL_IDX;
+	     current = getNextInSequence(current)) {
+		if (getNode(current) == node)
+			return true;
+		else if (getNode(current) == start)
+			continue;
+		else if (getUniqueness(getNode(current)))
+			return false;
+	}
+
+	return false;
+}
+
+static boolean comesFromNode(PassageMarkerI marker, Node * node)
+{
+	Node *source = getNode(getTwinMarker(marker));
+	Node *target = getTwinNode(node);
+	PassageMarkerI current;
+
+	for (current = getNextInSequence(getTwinMarker(marker)); current != NULL_IDX;
+	     current = getNextInSequence(current)) {
+		if (getNode(current) == target)
+			return true;
+		else if (getNode(current) == source) 
+			continue;
+		else if (getUniqueness(getNode(current)))
+			return false;
+	}
+
+	return false;
+}
+
+static void reconnectPassageMarker(PassageMarkerI marker, Node * node,
+				   PassageMarkerI * ptr)
+{
+	PassageMarkerI current;
+	PassageMarkerI next = getNextInSequence(marker);
+	PassageMarkerI tmpMarker;
+
+	for (current = marker; getNode(current) != node;
+	     current = getPreviousInSequence(current));
+
+	setPreviousInSequence(current, next);
+	concatenatePassageMarkers(current, marker);
+
+	// Removing node and all intermediaries
+	while (marker != current) {
+		tmpMarker = getPreviousInSequence(marker);
+		if (*ptr == marker || *ptr == getTwinMarker(marker))
+			*ptr = getNextInNode(*ptr);
+		setNextInSequence(marker, NULL_IDX);
+		setPreviousInSequence(NULL_IDX, marker);
+		destroyPassageMarker(marker);
+		marker = tmpMarker;
+	}
+}
+
+// DEBUG
+void checkNode(Node* node) {
+	PassageMarkerI marker1 = getMarker(node);
+
+	if (marker1 == NULL_IDX)
+		return;
+
+	PassageMarkerI marker2 = getNextInNode(marker1);
+
+	if (marker2 == NULL_IDX)
+		return;
+
+	if (getStartOffset(marker1) == getStartOffset(marker2))
+		abort();
+	if (getFinishOffset(marker1) == getFinishOffset(marker2))
+		abort();
+	printf(">>>> Node %li\n", (long) getNodeID(node));
+	printf("Marker1: %li - %li > %li (%li) \n", (long) getStartOffset(marker1), (long) getPassageMarkerLength(marker1), (long) (getNodeLength(node) - getFinishOffset(marker1)), (long) getFinishOffset(marker1));
+	printf("%s\n", readPassageMarker(marker1));
+	printf("Marker2: %li - %li > %li (%li) \n", (long) getStartOffset(marker2), (long) getPassageMarkerLength(marker2), (long) (getNodeLength(node) - getFinishOffset(marker2)), (long) getFinishOffset(marker2));
+
+	printf("%s\n", readPassageMarker(marker2));
+	if (getStartOffset(marker1) < getNodeLength(node) - getFinishOffset(marker2) 
+	    && getStartOffset(marker2) < getNodeLength(node) - getFinishOffset(marker1)) {
+		//abort();
+		;
+	}
+}
+
+static void concatenateLongReads(Node * node, Node * candidate,
+				 Graph * graph)
+{
+	PassageMarkerI marker, tmpMarker;
+
+	// Passage marker management in node:
+	for (marker = getMarker(node); marker != NULL_IDX;
+	     marker = getNextInNode(marker)) {
+		if (!goesToNode(marker, candidate))
+			incrementFinishOffset(marker,
+					      getNodeLength(candidate));
+	}
+
+	// Swapping new born passageMarkers from candidate to node
+	for (marker = getMarker(candidate); marker != NULL_IDX;
+	     marker = tmpMarker) {
+		tmpMarker = getNextInNode(marker);
+
+		if (!comesFromNode(marker, node)) {
+			extractPassageMarker(marker);
+			incrementStartOffset(marker,
+					      getNodeLength(node));
+			transposePassageMarker(marker, node);
+			incrementFinishOffset(getTwinMarker(marker),
+					      getNodeLength(node));
+		} else {
+			reconnectPassageMarker(marker, node, &tmpMarker);
+		}
+	}
+}
+
+static void adjustShortReadsByLength(Node * target, Coordinate nodeLength)
+{
+	ShortReadMarker *targetArray, *marker;
+	IDnum targetLength, index;
+	Coordinate position;
+
+	if (!readStartsAreActivated(graph))
+		return;
+
+	targetArray = getNodeReads(getTwinNode(target), graph);
+	targetLength = getNodeReadCount(getTwinNode(target), graph);
+
+	for (index = 0; index < targetLength; index++) {
+		marker = getShortReadMarkerAtIndex(targetArray, index);
+		position = getShortReadMarkerPosition(marker);
+		if (position != -1) {
+			position += nodeLength;
+			setShortReadMarkerPosition(marker, position);
+		}
+	}
+}
+
+static boolean abs_bool(boolean val)
+{
+	return val >= 0 ? val : -val;
+}
+
+static IDnum abs_ID(IDnum val)
+{
+	return val >= 0 ? val : -val;
+}
+
+static NodeList *pathIsClear(Node * node, Node * oppositeNode,
+			     Coordinate distance)
+{
+	Arc *arc;
+	Node *candidate, *dest, *current;
+	Coordinate extension_distance = 0;
+	boolean maxRepeat = 1;
+	Node *repeatEntrance = NULL;
+	IDnum counter = 0;
+	NodeList *path = NULL;
+	NodeList *tail = path;
+
+	setSingleNodeStatus(node, 2);
+
+	current = node;
+	while (true) {
+
+		//////////////////////////////////
+		//  Selecting destination       //
+		//////////////////////////////////
+		candidate = NULL;
+
+		// First round for priority nodes
+		for (arc = getArc(current); arc != NULL;
+		     arc = getNextArc(arc)) {
+			dest = getDestination(arc);
+
+			if (dest == node || dest == getTwinNode(node))
+				continue;
+
+			if (getNodeStatus(dest) <= 0)
+				continue;
+
+			if (candidate == NULL
+			    || getNodeStatus(candidate) >
+			    getNodeStatus(dest)
+			    || (getNodeStatus(candidate) ==
+				getNodeStatus(dest)
+				&& extension_distance >
+				localScaffold[getNodeID(dest) +
+					      nodeCount(graph)].
+				distance - getNodeLength(dest) / 2)) {
+				extension_distance =
+				    localScaffold[getNodeID(dest) +
+						  nodeCount(graph)].
+				    distance - getNodeLength(dest) / 2;
+				candidate = dest;
+			}
+		}
+
+		// In case of failure   
+		if (candidate == NULL) {
+			for (arc = getArc(current); arc != NULL;
+			     arc = getNextArc(arc)) {
+				dest = getDestination(arc);
+
+				if (getNodeStatus(dest) == 0)
+					continue;
+
+				if (dest == node
+				    || dest == getTwinNode(node))
+					continue;
+
+				if (candidate == NULL
+				    || getNodeStatus(candidate) <
+				    getNodeStatus(dest)
+				    || (getNodeStatus(candidate) ==
+					getNodeStatus(dest)
+					&& extension_distance <
+					localScaffold[getNodeID(dest) +
+						      nodeCount(graph)].
+					distance -
+					getNodeLength(dest) / 2)) {
+					extension_distance =
+					    localScaffold[getNodeID(dest) +
+							  nodeCount
+							  (graph)].
+					    distance -
+					    getNodeLength(dest) / 2;
+					candidate = dest;
+				}
+			}
+		}
+		if (candidate == NULL) {
+			while (path) {
+				tail = path->next;
+				deallocateNodeList(path);
+				path = tail;
+			}
+			return false;
+		}
+		// Loop detection
+		if (candidate == repeatEntrance
+		    && abs_bool(getNodeStatus(candidate)) ==
+		    maxRepeat + 1) {
+			while (path) {
+				tail = path->next;
+				deallocateNodeList(path);
+				path = tail;
+			}
+			return false;
+		} else if (abs_bool(getNodeStatus(candidate)) > maxRepeat) {
+			maxRepeat = abs_bool(getNodeStatus(candidate));
+			repeatEntrance = candidate;
+		} else if (abs_bool(getNodeStatus(candidate)) == 1) {
+			maxRepeat = 1;
+			repeatEntrance = NULL;
+		}
+
+		if (getNodeStatus(candidate) > 0)
+			setSingleNodeStatus(candidate,
+					    getNodeStatus(candidate) + 1);
+		else
+			setSingleNodeStatus(candidate,
+					    getNodeStatus(candidate) - 1);
+
+
+		if (abs_bool(getNodeStatus(candidate)) > 100
+		    || counter > nodeCount(graph)) {
+			while (path) {
+				tail = path->next;
+				deallocateNodeList(path);
+				path = tail;
+			}
+			return false;
+		}
+
+		// Missassembly detection
+		if (getUniqueness(candidate) && oppositeNode
+		    && candidate != oppositeNode
+		    && extension_distance > distance) {
+			while (path) {
+				tail = path->next;
+				deallocateNodeList(path);
+				path = tail;
+			}
+			return false;
+		}
+
+		if (path == NULL) {
+			path = allocateNodeList();
+			path->next = NULL;
+			path->node = candidate;
+			tail = path;
+		} else {
+			tail->next = allocateNodeList();
+			tail = tail->next;
+			tail->node = candidate;
+			tail->next = NULL;
+		}
+
+		if (getUniqueness(candidate))
+			return path;
+
+		current = candidate;
+	}
+}
+
+static boolean pushNeighbours(Node * node, Node * oppositeNode,
+			      Coordinate distance, boolean force_jumps)
+{
+	Node *candidate;
+	Coordinate oldLength = getNodeLength(node);
+	MiniConnection *localConnect;
+	NodeList *path, *tmp;
+
+	if ((path = pathIsClear(node, oppositeNode, distance))) {
+		while (path) {
+			candidate = path->node;
+			tmp = path->next;
+			deallocateNodeList(path);
+			path = tmp;
+
+			///////////////////////////////////////
+			//  Stepping forward to destination  //
+			///////////////////////////////////////
+
+			if (getUniqueness(candidate)) {
+				concatenateReadStarts(node, candidate,
+						      graph);
+				concatenateLongReads(node, candidate,
+						     graph);
+				absorbExtension(node, candidate);
+
+				// Scaffold changes
+				recenterNode(node, oldLength);
+				recenterLocalScaffold(node, oldLength);
+				absorbExtensionInScaffold(node, candidate);
+
+				// Read coverage
+#ifndef SINGLE_COV_CAT
+				Category cat;
+				for (cat = 0; cat < CATEGORIES; cat++) {
+					incrementVirtualCoverage(node, cat,
+								 getVirtualCoverage(candidate, cat));
+					incrementOriginalVirtualCoverage(node, cat,
+									 getOriginalVirtualCoverage(candidate, cat));
+				}
+#else
+				incrementVirtualCoverage(node, getVirtualCoverage(candidate));
+#endif
+
+				if (getNodeStatus(candidate)) {
+					localConnect =
+					    &localScaffold[getNodeID
+							   (candidate) +
+							   nodeCount
+							   (graph)];
+					if (localConnect->frontReference) {
+						destroyConnection
+						    (localConnect->
+						     frontReference,
+						     getNodeID(node));
+						localConnect->
+						    frontReference = NULL;
+					}
+					if (localConnect->backReference) {
+						destroyConnection
+						    (localConnect->
+						     backReference,
+						     -getNodeID(node));
+						localConnect->
+						    backReference = NULL;
+					}
+					unmarkNode(candidate,
+						   localConnect);
+				}
+				if (getNodeStatus(getTwinNode(candidate))) {
+					localConnect =
+					    &localScaffold[-getNodeID
+							   (candidate) +
+							   nodeCount
+							   (graph)];
+					if (localConnect->frontReference) {
+						destroyConnection
+						    (localConnect->
+						     frontReference,
+						     getNodeID(node));
+						localConnect->
+						    frontReference = NULL;
+					}
+					if (localConnect->backReference) {
+						destroyConnection
+						    (localConnect->
+						     backReference,
+						     -getNodeID(node));
+						localConnect->
+						    backReference = NULL;
+					}
+					unmarkNode(getTwinNode(candidate),
+						   localConnect);
+				}
+				destroyNode(candidate, graph);
+				return true;
+			} else {
+				adjustShortReads(node, candidate);
+				adjustLongReads(node, getNodeLength(candidate));
+				absorbExtension(node, candidate);
+			}
+		}
+	}
+
+	if (force_jumps && oppositeNode
+	    && abs_ID(getNodeID(oppositeNode)) < abs_ID(getNodeID(node))) {
+		distance -= getNodeLength(node) / 2;
+		distance -= getNodeLength(oppositeNode) / 2;
+		if (distance > 10) {
+			adjustShortReadsByLength(node, distance);
+			adjustLongReads(node, distance);
+			appendGap(node, distance, graph);
+		} else {
+			adjustShortReadsByLength(node, 10);
+			adjustLongReads(node, 10);
+			appendGap(node, 10, graph);
+		}
+
+		concatenateReadStarts(node, oppositeNode, graph);
+		concatenateLongReads(node, oppositeNode, graph);
+		absorbExtension(node, oppositeNode);
+
+		// Scaffold changes
+		recenterNode(node, oldLength);
+		recenterLocalScaffold(node, oldLength);
+		absorbExtensionInScaffold(node, oppositeNode);
+
+		// Read coverage
+#ifndef SINGLE_COV_CAT
+		Category cat;
+		for (cat = 0; cat < CATEGORIES; cat++)
+			incrementVirtualCoverage(node, cat,
+						 getVirtualCoverage(oppositeNode, cat));
+#else
+		incrementVirtualCoverage(node, getVirtualCoverage(oppositeNode));
+#endif
+
+		if (getNodeStatus(oppositeNode)) {
+			localConnect =
+			    &localScaffold[getNodeID(oppositeNode) +
+					   nodeCount(graph)];
+			if (localConnect->frontReference) {
+				destroyConnection(localConnect->
+						  frontReference,
+						  getNodeID(node));
+				localConnect->frontReference = NULL;
+			}
+			if (localConnect->backReference) {
+				destroyConnection(localConnect->
+						  backReference,
+						  -getNodeID(node));
+				localConnect->backReference = NULL;
+			}
+			unmarkNode(oppositeNode, localConnect);
+		}
+		if (getNodeStatus(getTwinNode(oppositeNode))) {
+			localConnect =
+			    &localScaffold[-getNodeID(oppositeNode) +
+					   nodeCount(graph)];
+			if (localConnect->frontReference) {
+				destroyConnection(localConnect->
+						  frontReference,
+						  getNodeID(node));
+				localConnect->frontReference = NULL;
+			}
+			if (localConnect->backReference) {
+				destroyConnection(localConnect->
+						  backReference,
+						  -getNodeID(node));
+				localConnect->backReference = NULL;
+			}
+			unmarkNode(getTwinNode(oppositeNode),
+				   localConnect);
+		}
+
+		destroyNode(oppositeNode, graph);
+	}
+
+	return false;
+}
+
+static void unmarkInterestingNodes()
+{
+	Node *node;
+	MiniConnection *localConnect;
+
+	while ((node = popNodeRecord())) {
+		setSingleNodeStatus(node, false);
+		localConnect =
+		    &localScaffold[getNodeID(node) + nodeCount(graph)];
+		localConnect->frontReference = NULL;
+		localConnect->backReference = NULL;
+		localConnect->nodeList = NULL;
+	}
+}
+
+static void findOppositeNode(Node * node, Node ** oppositeNode,
+			     Coordinate * distance)
+{
+	NodeList *nodeList;
+	MiniConnection *localConnect;
+	Node *node2;
+	IDnum node2ID;
+
+	*oppositeNode = NULL;
+	*distance = 0;
+
+	for (nodeList = markedNodes; nodeList != NULL;
+	     nodeList = nodeList->next) {
+		node2 = nodeList->node;
+		node2ID = getNodeID(node2);
+		localConnect = &localScaffold[node2ID + nodeCount(graph)];
+
+		if (node2 == node)
+			continue;
+
+		if (!getUniqueness(node2))
+			continue;
+
+		if (localConnect->distance < 0)
+			continue;
+
+		if (*oppositeNode == NULL
+		    || *distance > localConnect->distance) {
+			*oppositeNode = node2;
+			*distance = localConnect->distance;
+		}
+	}
+}
+
+static boolean expandLongNode(Node * node, boolean force_jumps)
+{
+	boolean hit = true;
+	boolean modified = false;
+	Node *oppositeNode;
+	Coordinate distance = 0;
+
+	markInterestingNodes(node);
+
+	while (hit) {
+		correctGraphLocally(node);
+		findOppositeNode(node, &oppositeNode, &distance);
+		hit =
+		    pushNeighbours(node, oppositeNode, distance,
+				   force_jumps);
+		modified = modified || hit;
+	}
+
+	unmarkInterestingNodes();
+
+	return modified;
+}
+
+static boolean expandLongNodes(boolean force_jumps)
+{
+	IDnum nodeID;
+	Node *node;
+	boolean modified = false;
+
+	for (nodeID = 1; nodeID <= nodeCount(graph); nodeID++) {
+		node = getNodeInGraph(graph, nodeID);
+
+		if (node != NULL && getUniqueness(node)) {
+			modified = expandLongNode(node, force_jumps)
+			    || modified;
+			modified =
+			    expandLongNode(getTwinNode(node), force_jumps)
+			    || modified;
+		}
+	}
+
+	return modified;
+}
+
+static void cleanMemory()
+{
+	velvetLog("Cleaning memory\n");
+
+	cleanScaffoldMemory();
+
+	destroyRecycleBin(nodeListMemory);
+	nodeListMemory = NULL;
+
+	free(localScaffold);
+}
+
+void exploitShortReadPairs(Graph * argGraph,
+			   ReadSet * reads,
+			   boolean * dubious,
+			   boolean * shadows,
+			   boolean force_jumps)
+{
+	boolean modified = true;
+
+	graph = argGraph;
+
+	if (!readStartsAreActivated(graph))
+		return;
+
+	velvetLog("Starting pebble resolution...\n");
+
+	resetNodeStatus(graph);
+
+	// Prepare scaffold
+	buildScaffold(graph, reads, dubious, shadows);
+
+	// Prepare graph
+	prepareGraphForLocalCorrections(graph);
+
+	// Prepare local scaffold 
+	localScaffold =
+	    callocOrExit(2 * nodeCount(graph) + 1, MiniConnection);
+
+	// Loop until convergence
+	while (modified)
+		modified = expandLongNodes(force_jumps);
+
+	// Clean up memory
+	cleanMemory();
+	deactivateLocalCorrectionSettings();
+
+	sortGapMarkers(graph);
+
+	velvetLog("Pebble done.\n");
+}