finishm 0.0.1

data/ext/src/src/passageMarker.h

@@ -0,0 +1,137 @@
+/*
+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 _PASSAGEMARKER_H_
+#define _PASSAGEMARKER_H_
+
+struct passageList_st {
+	PassageMarkerI marker;
+	PassageMarkerList *next;
+}  ATTRIBUTE_PACKED;
+
+///////////////////////////////////////////////////////////////////
+// PassageMarker lists
+///////////////////////////////////////////////////////////////////
+// You can always malloc a PassaegMarkerList but these routines manage the 
+// memory for you, thus avoiding fragmentation
+PassageMarkerList *newPassageMarkerList(PassageMarkerI marker,
+					PassageMarkerList * next);
+
+void deallocatePassageMarkerList(PassageMarkerList * list);
+
+///////////////////////////////////////////////////////////////////
+// Creators/Destructors
+///////////////////////////////////////////////////////////////////
+PassageMarkerI addPassageMarker(IDnum sequenceID, Coordinate start,
+				Node * node);
+
+PassageMarkerI addUncertainPassageMarker(IDnum sequenceID, Node * node);
+
+PassageMarkerI newPassageMarker(IDnum seqID, Coordinate start,
+				Coordinate finish, Coordinate startOffset,
+				Coordinate finishOffset);
+
+// Deallocates but also removes all pointers towards that structure
+void destroyPassageMarker(PassageMarkerI marker);
+void destroyAllPassageMarkers();
+
+///////////////////////////////////////////////////////////////////
+// Node 
+///////////////////////////////////////////////////////////////////
+
+// Current node
+Node *getNode(PassageMarkerI marker);
+
+// Yank out of current node
+void extractPassageMarker(PassageMarkerI marker);
+
+// Insert into a node
+void transposePassageMarker(PassageMarkerI marker, Node * destination);
+
+///////////////////////////////////////////////////////////////////
+// General Info
+///////////////////////////////////////////////////////////////////
+// Export into file
+void exportMarker(FILE * outfile, PassageMarkerI marker,
+		  TightString * sequences, int wordLength);
+
+// General info for debugging
+char *readPassageMarker(PassageMarkerI marker);
+
+// Sequence ID associated to the passage marker
+IDnum getPassageMarkerSequenceID(PassageMarkerI marker);
+IDnum getAbsolutePassMarkerSeqID(PassageMarkerI marker);
+int passageMarkerDirection(PassageMarkerI marker);
+
+// Coordinates
+Coordinate getPassageMarkerStart(PassageMarkerI marker);
+void setPassageMarkerStart(PassageMarkerI marker, Coordinate start);
+Coordinate getPassageMarkerFinish(PassageMarkerI marker);
+void setPassageMarkerFinish(PassageMarkerI marker, Coordinate finish);
+Coordinate getPassageMarkerLength(PassageMarkerI marker);
+
+// Offsets
+Coordinate getStartOffset(PassageMarkerI marker);
+void setStartOffset(PassageMarkerI marker, Coordinate offset);
+void incrementStartOffset(PassageMarkerI marker, Coordinate offset);
+Coordinate getFinishOffset(PassageMarkerI marker);
+void setFinishOffset(PassageMarkerI marker, Coordinate offset);
+void incrementFinishOffset(PassageMarkerI marker, Coordinate offset);
+
+// Status
+void setPassageMarkerStatus(PassageMarkerI marker, boolean status);
+boolean getPassageMarkerStatus(PassageMarkerI marker);
+
+///////////////////////////////////////////////////////////////////
+// Marker Sequences
+///////////////////////////////////////////////////////////////////
+
+// Corresponding marker of reverse complement sequence
+PassageMarkerI getTwinMarker(PassageMarkerI marker);
+
+// Within a node
+PassageMarkerI getNextInNode(PassageMarkerI marker);
+void setNextInNode(PassageMarkerI marker, PassageMarkerI next);
+void setTopOfTheNode(PassageMarkerI marker);
+
+// Within a sequence
+PassageMarkerI getNextInSequence(PassageMarkerI marker);
+void setNextInSequence(PassageMarkerI previous, PassageMarkerI next);
+PassageMarkerI getPreviousInSequence(PassageMarkerI marker);
+void setPreviousInSequence(PassageMarkerI previous, PassageMarkerI next);
+void connectPassageMarkers(PassageMarkerI previous, PassageMarkerI next,
+			   Graph * graph);
+
+// End of read chains
+boolean isTerminal(PassageMarkerI marker);
+boolean isInitial(PassageMarkerI marker);
+
+// Checks whether the node of the next marker is the one given in parameter
+boolean isDestinationToMarker(PassageMarkerI marker, Node * node);
+
+// Bypasses the middle marker
+void disconnectNextPassageMarker(PassageMarkerI marker, Graph * graph);
+void deleteNextPassageMarker(PassageMarkerI marker, Graph * graph);
+
+// Merge two markers (cf concatenateGraph())
+void concatenatePassageMarkers(PassageMarkerI marker,
+			       PassageMarkerI nextMarker);
+
+#endif

data/ext/src/src/preGraph.c

@@ -0,0 +1,1717 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#include "globals.h"
+#include "allocArray.h"
+#include "preGraph.h"
+#include "recycleBin.h"
+#include "tightString.h"
+#include "run.h"
+#include "utility.h"
+
+#define ADENINE 0
+#define CYTOSINE 1
+#define GUANINE 2
+#define THYMINE 3
+
+struct preMarker_st {
+	PreMarker * previous;
+	PreMarker * next;
+	IDnum referenceStart;
+	IDnum preNodeStart;
+	IDnum length;
+	IDnum referenceID;
+	IDnum preNodeID; /* SF TODO only the sign seems to matter. Could replace with char or bit field */
+} ATTRIBUTE_PACKED;
+
+typedef struct preArc_st PreArc;
+
+struct preArc_st {
+	PreArcI nextLeft; /* Index of the previous PreArc */
+	PreArcI nextRight; /* Index of the next PreArc */
+	IDnum multiplicity;
+	IDnum preNodeIDLeft;
+	IDnum preNodeIDRight;
+} ATTRIBUTE_PACKED;
+
+struct preNode_st {
+	PreArcI preArcLeft;
+	PreArcI preArcRight;
+	Descriptor *descriptor;
+	IDnum length;
+}  ATTRIBUTE_PACKED;
+
+struct preGraph_st {
+	PreNode *preNodes;
+	IDnum * nodeReferenceMarkerCounts;
+	PreMarker ** nodeReferenceMarkers;
+	IDnum sequenceCount;
+	IDnum referenceCount;
+	IDnum preNodeCount;
+	int wordLength;
+	boolean double_strand;
+};
+
+static AllocArray *preArcMemory = NULL;
+
+DECLARE_FAST_ACCESSORS(PREARC, PreArc, preArcMemory)
+
+PreArcI allocatePreArc_pg()
+{
+#ifdef _OPENMP
+	return allocArrayArrayAllocate (preArcMemory); 
+#else
+	if (preArcMemory == NULL)
+		preArcMemory = newAllocArray(sizeof(PreArc), "PreArc");
+	return allocArrayAllocate (preArcMemory);
+#endif
+
+}
+
+void deallocatePreArc_pg(PreArcI preArc)
+{
+#ifdef _OPENMP
+	allocArrayArrayFree (preArcMemory, preArc);
+#else
+	allocArrayFree (preArcMemory, preArc);
+#endif
+}
+
+// Returns the length of the preNode's descriptor list
+Coordinate getPreNodeLength_pg(IDnum preNodeID, PreGraph * preGraph)
+{
+	IDnum ID = preNodeID;
+
+	if (ID < 0)
+		ID = -ID;
+
+	return (preGraph->preNodes[ID]).length;
+}
+
+// Returns the number of preNodes in the preGraph
+IDnum preNodeCount_pg(PreGraph * preGraph)
+{
+	return preGraph->preNodeCount;
+}
+
+// returns the number of sequences used to buid the preGraph
+IDnum sequenceCount_pg(PreGraph * preGraph)
+{
+	return preGraph->sequenceCount;
+}
+
+PreArcI getPreArcBetweenPreNodes_pg(IDnum originPreNodeID,
+				    IDnum destinationPreNodeID,
+				    PreGraph * preGraph)
+{
+	PreArcI preArc;
+
+	if (originPreNodeID == 0 || destinationPreNodeID == 0) {
+		return NULL_IDX;
+	}
+
+	for (preArc = getPreArc_pg(originPreNodeID, preGraph);
+	     preArc != NULL_IDX;
+	     preArc = getNextPreArc_pg(preArc, originPreNodeID)) {
+		if (getDestination_pg(preArc, originPreNodeID) ==
+		    destinationPreNodeID) {
+			return preArc;
+		}
+	}
+
+	return NULL_IDX;
+}
+
+static void addPreArcToPreNode_pg(PreArcI preArc, IDnum preNodeID,
+				  PreGraph * preGraph)
+{
+	IDnum ID = preNodeID;
+	PreNode *preNode;
+	PreArcI *preArcPtr;
+	PreArc *preArcVal;
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	if (preNodeID > 0)
+		preArcPtr = &(preNode->preArcRight);
+	else
+		preArcPtr = &(preNode->preArcLeft);
+
+	preArcVal = PREARC_I2P (preArc);
+	preArcVal = PREARC_I2P (preArc);
+
+	if (preNodeID == preArcVal->preNodeIDLeft) {
+		preArcVal->nextLeft = *preArcPtr;
+		*preArcPtr = preArc;
+	}
+
+	if (preNodeID == preArcVal->preNodeIDRight) {
+		preArcVal->nextRight = *preArcPtr;
+		*preArcPtr = preArc;
+	}
+}
+
+// Creates an preArc from preNode origin to preNode destination.
+// If this preArc already exists, increments its multiplicity by 1.
+PreArcI createPreArc_pg(IDnum originPreNodeID, IDnum destinationPreNodeID,
+			PreGraph * preGraph)
+{
+	PreArcI preArc;
+	PreArc *preArcVal;
+
+
+	if (originPreNodeID == 0 || destinationPreNodeID == 0)
+		return NULL_IDX;
+
+	preArc =
+	    getPreArcBetweenPreNodes_pg(originPreNodeID,
+					destinationPreNodeID, preGraph);
+
+	if (preArc != NULL_IDX) {
+		PREARC_FI2P (preArc)->multiplicity++;
+		if (destinationPreNodeID == -originPreNodeID) 
+			PREARC_FI2P (preArc)->multiplicity++;
+		return preArc;
+	}
+	// If not found
+	preArc = allocatePreArc_pg();
+	preArcVal = PREARC_FI2P (preArc);
+	preArcVal->preNodeIDLeft = originPreNodeID;
+	preArcVal->preNodeIDRight = -destinationPreNodeID;
+	preArcVal->multiplicity = 1;
+
+	addPreArcToPreNode_pg(preArc, originPreNodeID, preGraph);
+
+	// Hairpin case
+	if (destinationPreNodeID == -originPreNodeID) {
+		preArcVal->multiplicity++;
+		return preArc;
+	}
+
+	addPreArcToPreNode_pg(preArc, -destinationPreNodeID, preGraph);
+
+	return preArc;
+}
+
+void createAnalogousPreArc_pg(IDnum originPreNodeID,
+			      IDnum destinationPreNodeID,
+			      PreArcI refPreArc, PreGraph * preGraph)
+{
+	PreArcI preArc;
+	PreArc *preArcVal;
+
+	if (originPreNodeID == 0 || destinationPreNodeID == 0)
+		return;
+
+	preArc =
+	    getPreArcBetweenPreNodes_pg(originPreNodeID,
+					destinationPreNodeID, preGraph);
+
+	if (preArc != NULL_IDX) {
+		PREARC_FI2P (preArc)->multiplicity += PREARC_FI2P (refPreArc)->multiplicity;
+		return;
+	}
+	// If not found
+	preArc = allocatePreArc_pg();
+	preArcVal = PREARC_FI2P (preArc);
+	preArcVal->preNodeIDLeft = originPreNodeID;
+	preArcVal->preNodeIDRight = -destinationPreNodeID;
+	preArcVal->multiplicity = PREARC_FI2P (refPreArc)->multiplicity;
+
+	addPreArcToPreNode_pg(preArc, originPreNodeID, preGraph);
+
+	// Hairpin case
+	if (destinationPreNodeID == -originPreNodeID)
+		return;
+
+	addPreArcToPreNode_pg(preArc, -destinationPreNodeID, preGraph);
+}
+
+static void setNextPreArc_pg(PreArcI preArc, IDnum preNodeID,
+			     PreArcI nextPreArc)
+{
+	PreArc *preArcVal;
+
+	preArcVal = PREARC_FI2P (preArc);
+	if (preNodeID == preArcVal->preNodeIDLeft)
+		preArcVal->nextLeft = nextPreArc;
+	if (preNodeID == preArcVal->preNodeIDRight)
+		preArcVal->nextRight = nextPreArc;
+}
+
+void removePreArcFromList_pg(PreArcI preArc, IDnum preNodeID,
+			     PreGraph * preGraph)
+{
+	IDnum ID = preNodeID;
+	PreNode *preNode;
+	PreArcI *preArcPtr;
+	PreArcI tempPreArc;
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	if (preNodeID > 0)
+		preArcPtr = &(preNode->preArcRight);
+	else
+		preArcPtr = &(preNode->preArcLeft);
+
+	if (*preArcPtr == preArc) {
+		*preArcPtr = getNextPreArc_pg(preArc, preNodeID);
+		return;
+	}
+
+	for (tempPreArc = *preArcPtr; tempPreArc != NULL_IDX;
+	     tempPreArc = getNextPreArc_pg(tempPreArc, preNodeID))
+		if (getNextPreArc_pg(tempPreArc, preNodeID) == preArc)
+			setNextPreArc_pg(tempPreArc, preNodeID,
+					 getNextPreArc_pg(preArc,
+							  preNodeID));
+}
+
+void destroyPreArc_pg(PreArcI preArc, PreGraph * preGraph)
+{
+	IDnum leftID, rightID;
+	PreArc *preArcVal;
+
+	if (preArc == NULL_IDX)
+		return;
+
+	preArcVal = PREARC_FI2P (preArc);
+	leftID = preArcVal->preNodeIDLeft;
+	rightID = preArcVal->preNodeIDRight;
+
+	// Removing preArc from list
+	removePreArcFromList_pg(preArc, leftID, preGraph);
+
+	// Removing preArc's twin from list
+	if (rightID != leftID)
+		removePreArcFromList_pg(preArc, rightID, preGraph);
+
+	deallocatePreArc_pg(preArc);
+}
+
+void destroyPreNode_pg(IDnum preNodeID, PreGraph * preGraph)
+{
+	PreNode *preNode;
+	IDnum ID = preNodeID;
+	IDnum index;
+	PreMarker * preMarker;
+
+	//velvetLog("Destroying %ld\n", (long) preNodeID);
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	// PreNode preArcs:
+	while (preNode->preArcLeft != NULL_IDX)
+		destroyPreArc_pg(preNode->preArcLeft, preGraph);
+	while (preNode->preArcRight != NULL_IDX)
+		destroyPreArc_pg(preNode->preArcRight, preGraph);
+
+	// PreMarkers
+	if (preGraph->nodeReferenceMarkers) {
+		for (index = 0; index < preGraph->nodeReferenceMarkerCounts[ID]; index++) {
+			preMarker = &(preGraph->nodeReferenceMarkers[ID][index]);
+			if (preMarker->previous != NULL)
+				preMarker->previous->next = NULL;
+			if (preMarker->next != NULL)
+				preMarker->next->previous = NULL;
+			preMarker->preNodeID = 0;
+			preMarker->referenceID = 0;
+		}
+		if (preGraph->nodeReferenceMarkers[ID]) 
+			free(preGraph->nodeReferenceMarkers[ID]);
+		preGraph->nodeReferenceMarkers[ID] = NULL;
+		preGraph->nodeReferenceMarkerCounts[ID] = 0;
+	}
+
+	// Descriptors
+	free(preNode->descriptor);
+
+	// Flag as destroyed
+	preNode->descriptor = NULL;
+}
+
+void destroyPreGraph_pg(PreGraph * preGraph)
+{
+	IDnum index;
+	PreNode *preNode = &(preGraph->preNodes[1]);
+
+	// Descriptors
+	for (index = 1; index <= preGraph->preNodeCount; index++) {
+		free(preNode->descriptor);
+		preNode++;
+	}
+
+	// Arcs
+#ifdef _OPENMP
+	destroyAllocArrayArray(preArcMemory);
+#else
+	destroyAllocArray(preArcMemory);
+#endif
+
+	// Nodes
+	free(preGraph->preNodes);
+
+        // PreMarkers
+        if (preGraph->nodeReferenceMarkerCounts) {
+                free(preGraph->nodeReferenceMarkerCounts);
+                free(preGraph->nodeReferenceMarkers);
+        }
+
+	// Graph
+	free(preGraph);
+
+}
+
+static Nucleotide getNucleotideInDescriptor_pg(Descriptor * descriptor,
+					       Coordinate i)
+{
+	Descriptor *fourMer = descriptor + i / 4;
+
+	switch (i % 4) {
+	case 0:
+		return (*fourMer & 3);
+	case 1:
+		return (*fourMer & 12) >> 2;
+	case 2:
+		return (*fourMer & 48) >> 4;
+	case 3:
+		return (*fourMer & 192) >> 6;
+	}
+	return 0;
+}
+
+PreNode *getPreNodeInPreGraph_pg(PreGraph * preGraph, IDnum preNodeID)
+{
+	PreNode *preNode;
+	if (preNodeID <= 0)
+		abort();
+	else {
+		preNode = &(preGraph->preNodes[preNodeID]);
+		if (preNode->descriptor != NULL)
+			return preNode;
+		else
+			return NULL;
+	}
+	return NULL;
+}
+
+PreArcI getPreArc_pg(IDnum preNodeID, PreGraph * preGraph)
+{
+	IDnum ID = preNodeID;
+	PreNode *preNode;
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	if (preNodeID > 0)
+		return preNode->preArcRight;
+	else
+		return preNode->preArcLeft;
+}
+
+PreArcI getNextPreArc_pg(PreArcI preArc, IDnum preNodeID)
+{
+	PreArc *preArcVal;
+
+	preArcVal = PREARC_FI2P (preArc);
+
+	if (preNodeID == preArcVal->preNodeIDLeft) {
+		return preArcVal->nextLeft;
+	} else {
+		return preArcVal->nextRight;
+	}
+}
+
+IDnum getMultiplicity_pg(PreArcI preArc)
+{
+	if (preArc == NULL_IDX)
+		return 0;
+
+	return PREARC_FI2P (preArc)->multiplicity;
+}
+
+IDnum getOtherEnd_pg(PreArcI preArc, IDnum preNodeID)
+{
+	PreArc *preArcVal;
+
+	preArcVal = PREARC_FI2P (preArc);
+	if (preNodeID == preArcVal->preNodeIDLeft)
+		return preArcVal->preNodeIDRight;
+	else
+		return preArcVal->preNodeIDLeft;
+}
+
+IDnum getDestination_pg(PreArcI preArc, IDnum preNodeID)
+{
+	PreArc *preArcVal;
+
+	if (preArc == NULL_IDX)
+		return 0;
+
+	preArcVal = PREARC_FI2P (preArc);
+
+	if (preNodeID == preArcVal->preNodeIDLeft)
+		return -preArcVal->preNodeIDRight;
+	else
+		return -preArcVal->preNodeIDLeft;
+}
+
+static void writeNucleotideInDescriptor_pg(Nucleotide nucleotide,
+					   Descriptor * descriptor,
+					   Coordinate i)
+{
+	Descriptor *fourMer = descriptor + i / 4;
+	switch (i % 4) {
+	case 3:
+		*fourMer &= 63;
+		*fourMer += nucleotide << 6;
+		return;
+	case 2:
+		*fourMer &= 207;
+		*fourMer += nucleotide << 4;
+		return;
+	case 1:
+		*fourMer &= 243;
+		*fourMer += nucleotide << 2;
+		return;
+	case 0:
+		*fourMer &= 252;
+		*fourMer += nucleotide;
+	}
+}
+
+static inline Descriptor *mergeDescriptors_pg(Descriptor * descr,
+					      Coordinate destinationLength,
+					      Descriptor * copy,
+					      Coordinate sourceLength,
+					      int wordLength)
+{
+	Descriptor *readPtr, *writePtr;
+	Descriptor readCopy = 0;
+	int readOffset, writeOffset;
+	size_t arrayLength;
+	Coordinate newLength =
+	    destinationLength + sourceLength + wordLength - 1;
+	Descriptor *new;
+	Coordinate index;
+
+	// Specify new array
+	arrayLength = newLength / 4;
+	if (newLength % 4)
+		arrayLength++;
+	new = callocOrExit(arrayLength, Descriptor);
+	for (index = 0; index < arrayLength; index++)
+		new[index] = 0;
+
+	// Copying first descriptor
+	readPtr = descr;
+	writePtr = new;
+	writeOffset = 0;
+	for (index = 0; index < destinationLength + wordLength - 1;
+	     index++) {
+		(*writePtr) >>= 2;
+		if (writeOffset == 0)
+			readCopy = *readPtr;
+		(*writePtr) += (readCopy & 3) << 6;
+
+		/*switch ((readCopy & 3)) {
+		   case ADENINE:
+		   velvetLog("A%ld", index);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C%ld", index);
+		   break;
+		   case GUANINE:
+		   velvetLog("G%ld", index);
+		   break;
+		   case THYMINE:
+		   velvetLog("T%ld", index);
+		   break;
+		   } */
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			readPtr++;
+			writeOffset = 0;
+		}
+	}
+
+	//velvetLog("\n");
+
+	// Skipping initial k-1 letters in second descriptor
+	readPtr = &(copy[(wordLength - 1) / 4]);
+	readCopy = *readPtr;
+	readOffset = (wordLength - 1) % 4;
+	readCopy >>= (readOffset * 2);
+
+	// Going on copying second descriptor
+	for (index = 0; index < sourceLength; index++) {
+		(*writePtr) >>= 2;
+		if (readOffset == 0)
+			readCopy = *readPtr;
+		(*writePtr) += (readCopy & 3) << 6;
+		/*switch ((readCopy & 3)) {
+		   case ADENINE:
+		   velvetLog("A%ld", index);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C%ld", index);
+		   break;
+		   case GUANINE:
+		   velvetLog("G%ld", index);
+		   break;
+		   case THYMINE:
+		   velvetLog("T%ld", index);
+		   break;
+		   default:
+		   velvetLog("?%ld;", index);
+		   } */
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			writeOffset = 0;
+		}
+
+		readOffset++;
+		if (readOffset == 4) {
+			readPtr++;
+			readOffset = 0;
+		}
+	}
+
+	//velvetLog("\n");
+
+	if (writeOffset != 0) {
+		while (writeOffset != 4) {
+			(*writePtr) >>= 2;
+			writeOffset++;
+		}
+	}
+
+	return new;
+}
+
+static inline Descriptor *mergeDescriptorsH2H_pg(Descriptor * descr,
+						 Coordinate
+						 destinationLength,
+						 Descriptor * copy,
+						 Coordinate sourceLength,
+						 int wordLength)
+{
+	Descriptor *readPtr, *writePtr;
+	Descriptor readCopy;
+	int readOffset, writeOffset;
+	size_t arrayLength;
+	Coordinate newLength =
+	    destinationLength + sourceLength + wordLength - 1;
+	Descriptor *new;
+	Coordinate index;
+
+	// Specify new array
+	arrayLength = newLength / 4;
+	if (newLength % 4)
+		arrayLength++;
+	new = callocOrExit(arrayLength, Descriptor);
+	for (index = 0; index < arrayLength; index++)
+		new[index] = 0;
+
+	// Copying first descriptor (including final (k-1)-mer)
+	readPtr = descr;
+	readCopy = *readPtr;
+	writePtr = new;
+	writeOffset = 0;
+	readOffset = 0;
+	for (index = 0; index < destinationLength + wordLength - 1;
+	     index++) {
+		(*writePtr) >>= 2;
+		if (writeOffset == 0)
+			readCopy = *readPtr;
+		(*writePtr) += (readCopy & 3) << 6;
+		/*switch ((readCopy & 3)) {
+		   case ADENINE:
+		   velvetLog("A(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case GUANINE:
+		   velvetLog("G(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case THYMINE:
+		   velvetLog("T(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   default:
+		   velvetLog("?(%ld %i %i);", index, writeOffset, readOffset);
+		   } */
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			readPtr++;
+			writeOffset = 0;
+		}
+	}
+
+	//velvetLog("\n");
+
+	// Going to end of second descriptor 
+	readPtr = &(copy[(sourceLength - 1) / 4]);
+	readCopy = *readPtr;
+	readOffset = (sourceLength - 1) % 4;
+	readCopy <<= ((3 - readOffset) * 2);
+
+	//velvetLog("Read copy %x\n", readCopy);
+
+	// Going on copying reverse complement of second descriptor
+	for (index = 0; index < sourceLength; index++) {
+		(*writePtr) >>= 2;
+		if (readOffset == 3)
+			readCopy = *readPtr;
+#ifndef COLOR
+		(*writePtr) += 192 - (readCopy & 192);
+#else
+		(*writePtr) += (readCopy & 192);
+#endif
+		/*switch (3 - ((readCopy & 192) >> 6)) {
+		   case ADENINE:
+		   velvetLog("A(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case GUANINE:
+		   velvetLog("G(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case THYMINE:
+		   velvetLog("T(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   default:
+		   velvetLog("?(%ld %i %i);", index, writeOffset, readOffset);
+		   } */
+		readCopy <<= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			writeOffset = 0;
+		}
+
+		readOffset--;
+		if (readOffset == -1) {
+			readPtr--;
+			readOffset = 3;
+		}
+	}
+
+	//velvetLog("\n");
+
+	if (writeOffset != 0) {
+		while (writeOffset != 4) {
+			(*writePtr) >>= 2;
+			writeOffset++;
+		}
+	}
+
+	return new;
+}
+
+static inline Descriptor *mergeDescriptorsF2F_pg(Descriptor * descr,
+						 Coordinate
+						 destinationLength,
+						 Descriptor * copy,
+						 Coordinate sourceLength,
+						 int wordLength)
+{
+	Descriptor *readPtr, *writePtr;
+	Descriptor readCopy;
+	int readOffset, writeOffset;
+	size_t arrayLength;
+	Coordinate newLength =
+	    destinationLength + sourceLength + wordLength - 1;
+	Descriptor *new;
+	Coordinate index;
+
+	// Specify new array
+	arrayLength = newLength / 4;
+	if (newLength % 4)
+		arrayLength++;
+	new = callocOrExit(arrayLength, Descriptor);
+	for (index = 0; index < arrayLength; index++)
+		new[index] = 0;
+
+	writePtr = new;
+	writeOffset = 0;
+
+	// Going to end of first descriptor 
+	readPtr = &(copy[(sourceLength + wordLength - 2) / 4]);
+	readCopy = *readPtr;
+	readOffset = (sourceLength + wordLength - 2) % 4;
+	readCopy <<= ((3 - readOffset) * 2);
+
+	// Copying reverse complement of first descriptor (minus final (k-1)-mer)
+	for (index = 0; index < sourceLength; index++) {
+		(*writePtr) >>= 2;
+		if (readOffset == 3)
+			readCopy = *readPtr;
+#ifndef COLOR
+		(*writePtr) += 192 - (readCopy & 192);
+#else
+		(*writePtr) += (readCopy & 192);
+#endif
+		/*switch (3 - ((readCopy & 192) >> 6)) {
+		   case ADENINE:
+		   velvetLog("A(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case GUANINE:
+		   velvetLog("G(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case THYMINE:
+		   velvetLog("T(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   default:
+		   velvetLog("?(%ld %i %i);", index, writeOffset, readOffset);
+		   } */
+		readCopy <<= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			writeOffset = 0;
+		}
+
+		readOffset--;
+		if (readOffset == -1) {
+			readPtr--;
+			readOffset = 3;
+		}
+	}
+
+	//velvetLog("\n");
+
+	// Going on copying second descriptor
+	readPtr = descr;
+	readCopy = *readPtr;
+	readOffset = 0;
+
+	for (index = 0; index < destinationLength + wordLength - 1;
+	     index++) {
+		(*writePtr) >>= 2;
+		if (readOffset == 0)
+			readCopy = *readPtr;
+		(*writePtr) += (readCopy & 3) << 6;
+		/*switch ((readCopy & 3)) {
+		   case ADENINE:
+		   velvetLog("A(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case CYTOSINE:
+		   velvetLog("C(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case GUANINE:
+		   velvetLog("G(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   case THYMINE:
+		   velvetLog("T(%ld %i %i) ", index, writeOffset, readOffset);
+		   break;
+		   default:
+		   velvetLog("?(%ld %i %i);", index, writeOffset, readOffset);
+		   } */
+		readCopy >>= 2;
+
+		writeOffset++;
+		if (writeOffset == 4) {
+			writePtr++;
+			writeOffset = 0;
+		}
+
+		readOffset++;
+		if (readOffset == 4) {
+			readPtr++;
+			readOffset = 0;
+		}
+	}
+
+	//velvetLog("\n");
+
+	if (writeOffset != 0) {
+		while (writeOffset != 4) {
+			(*writePtr) >>= 2;
+			writeOffset++;
+		}
+	}
+
+	return new;
+}
+
+void setMultiplicity_pg(PreArcI preArc, IDnum mult)
+{
+	PREARC_FI2P (preArc)->multiplicity = mult;
+}
+
+static void updatePreArcData_pg(PreArcI preArc, IDnum oldPreNodeID,
+				IDnum newPreNodeID)
+{
+	PreArc *preArcVal;
+
+	preArcVal = PREARC_FI2P (preArc);
+	if (preArcVal->preNodeIDLeft == oldPreNodeID)
+		preArcVal->preNodeIDLeft = newPreNodeID;
+	if (preArcVal->preNodeIDRight == oldPreNodeID)
+		preArcVal->preNodeIDRight = newPreNodeID;
+}
+
+// Reshuffles the preGraph->preNodes array to remove NULL pointers
+// Beware that preNode IDs are accordingly reshuffled (all pointers remain valid though)
+void renumberPreNodes_pg(PreGraph * preGraph)
+{
+	IDnum preNodeIndex;
+	PreNode *currentPreNode, *destinationPreNode;
+	IDnum counter = 0;
+	IDnum preNodes = preGraph->preNodeCount;
+	IDnum newIndex;
+	IDnum preMarkerIndex;
+	PreMarker * preMarker;
+	PreArcI preArc;
+
+	velvetLog("Renumbering preNodes\n");
+	velvetLog("Initial preNode count %li\n", (long) preGraph->preNodeCount);
+
+	for (preNodeIndex = 1; preNodeIndex <= preNodes; preNodeIndex++) {
+		currentPreNode = &(preGraph->preNodes[preNodeIndex]);
+
+		if (currentPreNode->descriptor == NULL)
+			counter++;
+		else if (counter != 0) {
+			newIndex = preNodeIndex - counter;
+			destinationPreNode =
+			    &(preGraph->preNodes[newIndex]);
+
+			destinationPreNode->preArcLeft =
+			    currentPreNode->preArcLeft;
+			destinationPreNode->preArcRight =
+			    currentPreNode->preArcRight;
+			destinationPreNode->descriptor =
+			    currentPreNode->descriptor;
+			destinationPreNode->length =
+			    currentPreNode->length;
+
+			for (preArc = getPreArc_pg(newIndex, preGraph);
+			     preArc != NULL_IDX;
+			     preArc = getNextPreArc_pg(preArc, newIndex))
+				updatePreArcData_pg(preArc, preNodeIndex,
+						    newIndex);
+			for (preArc = getPreArc_pg(-newIndex, preGraph);
+			     preArc != NULL_IDX;
+			     preArc = getNextPreArc_pg(preArc, -newIndex))
+				updatePreArcData_pg(preArc, -preNodeIndex,
+						    -newIndex);
+			
+			if (preGraph->nodeReferenceMarkers) {
+				preGraph->nodeReferenceMarkerCounts[newIndex] = preGraph->nodeReferenceMarkerCounts[preNodeIndex];
+				preGraph->nodeReferenceMarkers[newIndex] = preGraph->nodeReferenceMarkers[preNodeIndex];
+
+				for (preMarkerIndex = 0; preMarkerIndex < preGraph->nodeReferenceMarkerCounts[newIndex]; preMarkerIndex++) {
+					preMarker = &(preGraph->nodeReferenceMarkers[newIndex][preMarkerIndex]);
+					if (preMarker->preNodeID == preNodeIndex)
+						preMarker->preNodeID = newIndex;
+					else if (preMarker->preNodeID == -preNodeIndex)
+						preMarker->preNodeID = -newIndex;
+					else 
+						abort();
+				}
+			}
+		}
+	}
+
+	preGraph->preNodeCount -= counter;
+	preGraph->preNodes = reallocOrExit(preGraph->preNodes,
+				     preGraph->preNodeCount +
+				      1, PreNode);
+
+	velvetLog("Destroyed %li preNodes\n", (long) counter);
+}
+
+// Allocate memory for an empty preGraph created with sequenceCount different sequences
+PreGraph *emptyPreGraph_pg(IDnum sequenceCount, IDnum referenceCount, int wordLength, boolean double_strand)
+{
+	PreGraph *newPreGraph = mallocOrExit(1, PreGraph);
+	newPreGraph->sequenceCount = sequenceCount;
+	newPreGraph->wordLength = wordLength;
+	newPreGraph->preNodeCount = 0;
+	newPreGraph->double_strand = double_strand;
+	newPreGraph->referenceCount = referenceCount;
+	newPreGraph->preNodes = NULL;
+	newPreGraph->nodeReferenceMarkerCounts = NULL;
+	newPreGraph->nodeReferenceMarkers = NULL;
+
+#ifdef _OPENMP
+	preArcMemory = newAllocArrayArray(omp_get_max_threads(), sizeof(PreArc), "PreArc");
+#endif
+
+	return newPreGraph;
+}
+
+static Descriptor *newDescriptor_pg(Coordinate length, SequencesReader *seqReadInfo,
+				    Kmer * initialKmer, int wordLength)
+{
+	char letter;
+	Nucleotide nucleotide;
+	Coordinate totalLength = length + wordLength - 1;
+	size_t arrayLength = totalLength / 4;
+	Descriptor *res;
+	Coordinate index;
+	Kmer kmerCopy;
+
+	if (totalLength % 4 > 0)
+		arrayLength++;
+
+	res = callocOrExit(arrayLength, Descriptor);
+
+	copyKmers(&kmerCopy, initialKmer);
+	for (index = wordLength - 2; index >= 0; index--)
+		writeNucleotideInDescriptor_pg(popNucleotide(&kmerCopy), res,
+					       index);
+
+	for (index = wordLength - 1; index < totalLength; index++) {
+		if (seqReadInfo->m_bIsBinary) {
+			letter = **seqReadInfo->m_ppCurrString;
+			*seqReadInfo->m_ppCurrString += 1;   // increment the pointer
+		} else {
+			letter = getc(seqReadInfo->m_pFile);
+			while (!isalpha(letter))
+				letter = getc(seqReadInfo->m_pFile);
+		}
+		//velvetLog("%c", letter);
+		switch (letter) {
+		case 'N':
+		case 'A':
+			nucleotide = ADENINE;
+			break;
+		case 'C':
+			nucleotide = CYTOSINE;
+			break;
+		case 'G':
+			nucleotide = GUANINE;
+			break;
+		case 'T':
+			nucleotide = THYMINE;
+			break;
+		default:
+			fflush(stdout);
+			abort();
+		}
+
+		writeNucleotideInDescriptor_pg(nucleotide, res, index);
+		pushNucleotide(initialKmer, nucleotide);
+	}
+
+	//velvetLog(" ");
+
+	return res;
+}
+
+void allocatePreNodeSpace_pg(PreGraph * preGraph, IDnum preNodeCount)
+{
+	preGraph->preNodes = callocOrExit(preNodeCount + 1, PreNode);
+	preGraph->preNodeCount = preNodeCount;
+}
+
+void allocatePreMarkerCountSpace_pg(PreGraph * preGraph)
+{
+	preGraph->nodeReferenceMarkerCounts = callocOrExit(preGraph->preNodeCount + 1, IDnum);
+	preGraph->nodeReferenceMarkers = callocOrExit(preGraph->preNodeCount + 1, PreMarker *);
+}
+
+void incrementNodeReferenceMarkerCount_pg(PreGraph * preGraph, IDnum preNodeID) {
+	if (preNodeID < 0)
+		preNodeID = -preNodeID;
+
+	preGraph->nodeReferenceMarkerCounts[preNodeID]++;
+}
+
+void allocatePreMarkerSpace_pg(PreGraph * preGraph) {
+	IDnum index;
+	
+	if (!preGraph->nodeReferenceMarkers)
+		return;
+
+	for (index = 1; index <= preGraph->preNodeCount; index++) {
+		if (preGraph->nodeReferenceMarkerCounts[index])
+			preGraph->nodeReferenceMarkers[index] = callocOrExit(preGraph->nodeReferenceMarkerCounts[index], PreMarker);
+		else 
+			preGraph->nodeReferenceMarkers[index] = NULL;
+		preGraph->nodeReferenceMarkerCounts[index] = 0;
+	}
+}
+
+PreMarker * addPreMarker_pg(PreGraph * preGraph, IDnum nodeID, IDnum seqID, Coordinate * start, PreMarker * previous) {
+	PreMarker * preMarker;
+	IDnum positive_nodeID;
+
+	if (nodeID < 0) 
+		abort();
+	else
+		positive_nodeID = nodeID;
+
+	//printf("Adding preMarker %li\n", (long) *start);
+
+	preMarker = &(preGraph->nodeReferenceMarkers[positive_nodeID][(preGraph->nodeReferenceMarkerCounts[positive_nodeID])++]);
+	preMarker->previous = previous;
+	if (previous) 
+		previous->next = preMarker;
+	preMarker->next = NULL;
+	preMarker->referenceStart = *start;
+	preMarker->length = preGraph->preNodes[positive_nodeID].length;
+	preMarker->preNodeStart = 0;
+	preMarker->preNodeID = nodeID;
+	preMarker->referenceID = seqID;
+
+	*start += preMarker->length;
+
+	return preMarker;
+}
+void addPreNodeToPreGraph_pg(PreGraph * preGraph, Coordinate start,
+			     Coordinate finish, SequencesReader *seqReadInfo,
+			     Kmer * initialKmer, IDnum ID)
+{
+	PreNode *newnd = &(preGraph->preNodes[ID]);
+
+	newnd->preArcLeft = NULL_IDX;
+	newnd->preArcRight = NULL_IDX;
+
+	newnd->length = finish - start;
+
+	newnd->descriptor =
+	    newDescriptor_pg(newnd->length, seqReadInfo, initialKmer,
+			     preGraph->wordLength);
+}
+
+static void exportPreNode_pg(FILE * outfile, PreNode * preNode, IDnum ID,
+			     int wordLength)
+{
+	Coordinate index;
+	Nucleotide nucleotide;
+
+	if (preNode == NULL)
+		return;
+
+	velvetFprintf(outfile, "NODE\t%ld\t%lld\n", (long) ID, (long long) preNode->length);
+
+	if (preNode->length == 0) {
+		velvetFprintf(outfile, "\n");
+		return;
+	}
+
+	for (index = 0; index < preNode->length + wordLength - 1; index++) {
+		nucleotide =
+		    getNucleotideInDescriptor_pg(preNode->descriptor,
+						 index);
+		switch (nucleotide) {
+		case ADENINE:
+			velvetFprintf(outfile, "A");
+			break;
+		case CYTOSINE:
+			velvetFprintf(outfile, "C");
+			break;
+		case GUANINE:
+			velvetFprintf(outfile, "G");
+			break;
+		case THYMINE:
+			velvetFprintf(outfile, "T");
+			break;
+		}
+	}
+
+	velvetFprintf(outfile, "\n");
+}
+
+static void exportPreMarker(FILE * outfile, PreMarker* preMarker) {
+	velvetFprintf(outfile, "%li\t%lli\t%lli\t%lli\n", (long) preMarker->preNodeID, (long long) preMarker->preNodeStart, (long long) preMarker->referenceStart, (long long) preMarker->length);
+}
+
+static void exportPreReference_pg(FILE * outfile, IDnum refIndex, PreGraph * preGraph) {
+	PreMarker * preMarker;
+	IDnum nodeID, index;
+
+	velvetFprintf(outfile, "SEQ\t%li\n", (long) refIndex);
+
+	for (nodeID = 1; nodeID <= preGraph->preNodeCount; nodeID++) {
+		for (index = 0; index < preGraph->nodeReferenceMarkerCounts[nodeID]; index++) {
+			preMarker = &(preGraph->nodeReferenceMarkers[nodeID][index]);
+			if (preMarker->referenceID == refIndex && !preMarker->previous) {
+				for (;preMarker;preMarker = preMarker->next) {
+					exportPreMarker(outfile, preMarker);
+				}
+			}
+		}
+	}
+}
+
+void exportPreGraph_pg(char *filename, PreGraph * preGraph)
+{
+	IDnum index;
+	FILE *outfile;
+	PreNode *preNode;
+	int wordLength = getWordLength_pg(preGraph);
+
+	if (preGraph == NULL) {
+		return;
+	}
+
+	outfile = fopen(filename, "w");
+	if (outfile == NULL) {
+		velvetLog("Couldn't open file, sorry\n");
+		return;
+	} else
+		velvetLog("Writing into pregraph file %s...\n", filename);
+
+	// General data
+	velvetFprintf(outfile, "%ld\t%ld\t%i\t%hi\n", (long) preGraph->preNodeCount,
+		(long) preGraph->sequenceCount, preGraph->wordLength, (short) preGraph->double_strand);
+
+	// PreNode info
+	for (index = 1; index <= preGraph->preNodeCount; index++) {
+		preNode = getPreNodeInPreGraph_pg(preGraph, index);
+		exportPreNode_pg(outfile, preNode, index, wordLength);
+	}
+
+	// Reference sequence info
+	for (index = 1; index <= preGraph->referenceCount; index++)
+		exportPreReference_pg(outfile, index, preGraph);
+
+
+	fclose(outfile);
+}
+
+int getWordLength_pg(PreGraph * preGraph)
+{
+	return preGraph->wordLength;
+}
+
+boolean hasSinglePreArc_pg(IDnum preNodeID, PreGraph * preGraph)
+{
+	IDnum ID = preNodeID;
+	PreNode *preNode;
+	PreArcI preArc;
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	if (preNodeID > 0)
+		preArc = preNode->preArcRight;
+	else
+		preArc = preNode->preArcLeft;
+
+	return (preArc != NULL_IDX
+		&& getNextPreArc_pg(preArc, preNodeID) == NULL_IDX);
+}
+
+char simplePreArcCount_pg(IDnum preNodeID, PreGraph * preGraph)
+{
+	PreNode *preNode;
+	PreArcI preArc;
+	char count = 0;
+	IDnum ID = preNodeID;
+
+	if (ID < 0)
+		ID = -ID;
+
+	preNode = &(preGraph->preNodes[ID]);
+
+	if (preNodeID > 0)
+		preArc = preNode->preArcRight;
+	else
+		preArc = preNode->preArcLeft;
+
+	for (; preArc != NULL_IDX;
+	     preArc = getNextPreArc_pg(preArc, preNodeID))
+		count++;
+
+	return count;
+}
+
+boolean isLoop_pg(PreArcI preArc)
+{
+	PreArc *preArcVal = PREARC_FI2P (preArc);
+
+	return (preArcVal->preNodeIDLeft == preArcVal->preNodeIDRight
+		|| preArcVal->preNodeIDLeft == -preArcVal->preNodeIDRight);
+}
+
+void setPreNodeDescriptor_pg(Descriptor * descr, Coordinate length, IDnum preNodeID, PreGraph * preGraph) {
+	PreNode * preNode;
+
+	if (preNodeID < 0) 
+		preNodeID = -preNodeID;
+
+	preNode = getPreNodeInPreGraph_pg(preGraph, preNodeID);
+	free(preNode->descriptor);
+	preNode->descriptor = descr;
+	preNode->length = length;	
+}
+
+static void appendPositiveDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {
+	PreNode * preNode = getPreNodeInPreGraph_pg(preGraph, preNodeID);
+	Descriptor * readPtr = preNode->descriptor;
+	Descriptor readCopy;
+	int wordLength = getWordLength_pg(preGraph);
+	Coordinate length = preNode->length;
+	Coordinate index;
+	int readOffset = 0;
+
+	if (initial) {
+		index = 0;
+		readPtr = preNode->descriptor;
+		readCopy = *readPtr;
+		readOffset = 0;
+	} else {
+		index = wordLength - 1;
+		readPtr = &(preNode->descriptor[(wordLength - 1) / 4]);
+		readCopy = *readPtr;
+		readOffset = (wordLength - 1) % 4;
+		readCopy >>= (readOffset * 2);
+	}
+
+	for (; index < length + wordLength - 1; index++) {
+		(**writePtr) >>= 2;
+		if (readOffset == 0)
+			readCopy = *readPtr;
+		(**writePtr) += (readCopy & 3) << 6;
+		readCopy >>= 2;
+
+		if (++(*writeOffset) == 4) {
+			(*writePtr)++;
+			*writeOffset = 0;
+		}
+
+		if (++readOffset == 4) {
+			readPtr++;
+			readOffset = 0;
+		}
+	}
+}
+
+static void appendNegativeDescriptor_pg(Descriptor ** writePtr, int * writeOffset, IDnum preNodeID, PreGraph * preGraph, boolean initial) {
+	PreNode * preNode = getPreNodeInPreGraph_pg(preGraph, preNodeID);
+	Descriptor * readPtr = preNode->descriptor;
+	Descriptor readCopy;
+	int wordLength = getWordLength_pg(preGraph);
+	Coordinate length = preNode->length;
+	Coordinate index;
+	int readOffset;
+
+	if (initial) 
+		length += wordLength - 1;
+
+	readPtr = &(preNode->descriptor[(length - 1) / 4]);
+	readCopy = *readPtr;
+	readOffset = (length - 1) % 4;
+	readCopy <<= ((3 - readOffset) * 2);
+
+	for (index = 0; index < length; index++) {
+		(**writePtr) >>= 2;
+		if (readOffset == 3)
+			readCopy = *readPtr;
+#ifndef COLOR
+		(**writePtr) += 192 - (readCopy & 192);
+#else
+		(**writePtr) += (readCopy & 192);
+#endif
+		readCopy <<= 2;
+
+		(*writeOffset)++;
+		if (*writeOffset == 4) {
+			(*writePtr)++;
+			*writeOffset = 0;
+		}
+
+		readOffset--;
+		if (readOffset == -1) {
+			readPtr--;
+			readOffset = 3;
+		}
+	}
+}
+
+void appendDescriptors_pg(Descriptor ** start, int * writeOffset, IDnum preNodeID, PreGraph* preGraph, boolean initial) {
+	if (preNodeID > 0)
+		appendPositiveDescriptor_pg(start, writeOffset, preNodeID, preGraph, initial);
+	else
+		appendNegativeDescriptor_pg(start, writeOffset, -preNodeID, preGraph, initial);
+}
+
+boolean referenceMarkersAreActivated_pg(PreGraph * preGraph) {
+	return preGraph->nodeReferenceMarkers != NULL;
+}
+
+static void copyPreMarker(PreMarker * dest, PreMarker * source, IDnum preNodeAID, PreGraph * preGraph) {
+	dest->previous = source->previous;
+	dest->next = source->next;
+
+	dest->preNodeStart = source->preNodeStart;
+	dest->length = source->length;
+	dest->referenceID = source->referenceID;
+	dest->referenceStart = source->referenceStart;
+
+	if (source->preNodeID > 0)
+		dest->preNodeID = preNodeAID;
+	else 
+		dest->preNodeID = -preNodeAID;
+
+	if (source->previous)
+		source->previous->next = dest;
+	if (source->next)
+		source->next->previous = dest;
+
+	source->referenceID = 0;
+	source->preNodeID = 0;
+	source->previous = NULL;
+	source->next = NULL;
+}
+
+static PreMarker * reallocOrExitReferenceMarkers(PreGraph * preGraph, IDnum preNodeID, IDnum length) {
+	PreMarker * array = callocOrExit(length, PreMarker);
+	PreMarker * writer = array;
+	PreMarker * reader = preGraph->nodeReferenceMarkers[preNodeID];
+	IDnum index;
+
+	for (index = 0; index < preGraph->nodeReferenceMarkerCounts[preNodeID]; index++) {
+		copyPreMarker(writer, reader, preNodeID, preGraph);	
+		writer++;
+		reader++;
+	} 
+
+	free(preGraph->nodeReferenceMarkers[preNodeID]);
+
+	return array;
+}
+
+static void concatenateReferenceMarkers_H2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {
+	IDnum index;
+	IDnum countA = preGraph->nodeReferenceMarkerCounts[preNodeAID];
+	IDnum countB = preGraph->nodeReferenceMarkerCounts[preNodeBID];
+	Coordinate lengthA = preGraph->preNodes[preNodeAID].length + totalOffset;
+	PreMarker * markerA, *next, *markerB;
+	IDnum counter = 0;
+	
+	for (index = 0 ; index < countA; index++) {
+		markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][index]);
+
+		if (markerA->preNodeID > 0)
+			next = markerA->next;
+		else 
+			next = markerA->previous;
+
+		if (!next)
+			continue;
+
+		if (markerA->preNodeID == preNodeAID && next->preNodeID != preNodeBID)
+			continue;
+		if (markerA->preNodeID == -preNodeAID && next->preNodeID != -preNodeBID)
+			continue;
+
+		next->referenceID = 0;
+		next->preNodeID = 0;
+
+		markerA->length += next->length;
+		if (markerA->preNodeID > 0) {
+			markerA->next = next->next;
+			if (next->next) 
+				next->next->previous = markerA;
+		} else {
+			markerA->previous = next->previous;
+			if (next->previous)
+				next->previous->next = markerA;
+			markerA->referenceStart = next->referenceStart;
+		}
+		next->next = NULL;
+		next->previous = NULL;
+	}
+
+	for (index = 0; index < countB; index++) 
+		if (preGraph->nodeReferenceMarkers[preNodeBID][index].referenceID)
+			counter++;
+
+	if (counter == 0)
+		return;
+
+	if (countA)
+		preGraph->nodeReferenceMarkers[preNodeAID] = reallocOrExitReferenceMarkers(preGraph, preNodeAID, countA + counter);
+	else 
+		preGraph->nodeReferenceMarkers[preNodeAID] = callocOrExit(counter, PreMarker);
+
+	for (index = 0; index < countB; index++) {
+		markerB = &(preGraph->nodeReferenceMarkers[preNodeBID][index]);
+		if (markerB->referenceID) {
+			markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][countA++]);
+			copyPreMarker(markerA, markerB, preNodeAID, preGraph);
+			markerA->preNodeStart += lengthA;
+		}
+	}
+
+	preGraph->nodeReferenceMarkerCounts[preNodeAID] = countA;
+}
+
+static void concatenateReferenceMarkers_H2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {
+	IDnum index;
+	IDnum countA = preGraph->nodeReferenceMarkerCounts[preNodeAID];
+	IDnum countB = preGraph->nodeReferenceMarkerCounts[preNodeBID];
+	Coordinate lengthA = preGraph->preNodes[preNodeAID].length + totalOffset;
+	Coordinate lengthB = preGraph->preNodes[preNodeBID].length;
+	PreMarker * markerA, *next, *markerB;
+	IDnum counter = 0;
+
+	for (index = 0 ; index < countA; index++) {
+		markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][index]);
+
+		if (markerA->preNodeID > 0)
+			next = markerA->next;
+		else 
+			next = markerA->previous;
+
+		
+		if ((!next) 
+		    || (markerA->preNodeID == preNodeAID && next->preNodeID != -preNodeBID)
+		    || (markerA->preNodeID == -preNodeAID && next->preNodeID != preNodeBID))
+			continue;
+	
+		next->referenceID = 0;
+		next->preNodeID = 0;
+
+		markerA->length += next->length;
+		if (markerA->preNodeID > 0) {
+			markerA->next = next->next;
+			if (next->next)
+				next->next->previous = markerA;
+		} else {
+			markerA->previous = next->previous;
+			if (next->previous)
+				next->previous->next = markerA;
+			markerA->referenceStart = next->referenceStart;
+		}
+		next->next = NULL;
+		next->previous = NULL;
+	}
+
+	for (index = 0; index < countB; index++) 
+		if (preGraph->nodeReferenceMarkers[preNodeBID][index].referenceID)
+			counter++;
+
+	if (counter == 0)
+		return;
+
+	if (countA)
+		preGraph->nodeReferenceMarkers[preNodeAID] = reallocOrExitReferenceMarkers(preGraph, preNodeAID, countA + counter);
+	else
+		preGraph->nodeReferenceMarkers[preNodeAID] = callocOrExit(counter, PreMarker);
+
+	for (index = 0; index < countB; index++) {
+		markerB = &(preGraph->nodeReferenceMarkers[preNodeBID][index]);
+		if (markerB->referenceID) {
+			markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][countA++]);
+			copyPreMarker(markerA, markerB, preNodeAID, preGraph);
+			markerA->preNodeID *= -1;
+			markerA->preNodeStart = lengthA + lengthB - markerA->preNodeStart - markerA->length;
+		}
+	}
+
+	preGraph->nodeReferenceMarkerCounts[preNodeAID] = countA;
+}
+
+static void concatenateReferenceMarkers_T2T_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {
+	IDnum index;
+	IDnum countA = preGraph->nodeReferenceMarkerCounts[preNodeAID];
+	IDnum countB = preGraph->nodeReferenceMarkerCounts[preNodeBID];
+	Coordinate lengthB = preGraph->preNodes[preNodeBID].length;
+	PreMarker * markerA, *next, *markerB;
+	IDnum counter = 0;
+
+	for (index = 0 ; index < countA; index++) {
+		markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][index]);
+
+		if (markerA->preNodeID < 0)
+			next = markerA->next;
+		else 
+			next = markerA->previous;
+
+		if (!next 
+		    || (markerA->preNodeID == preNodeAID && next->preNodeID != -preNodeBID)
+		    || (markerA->preNodeID == -preNodeAID && next->preNodeID != preNodeBID)) {
+			markerA->preNodeStart += lengthB;
+			continue;
+		}
+
+		next->referenceID = 0;
+		next->preNodeID = 0;
+
+		markerA->length += next->length;
+		markerA->preNodeStart = lengthB - next->preNodeStart - next->length;
+		if (markerA->preNodeID < 0) {
+			markerA->next = next->next;
+			if (next->next)
+				next->next->previous = markerA;
+		} else {
+			markerA->previous = next->previous;
+			if (next->previous) 
+				next->previous->next = markerA;
+			markerA->referenceStart = next->referenceStart;
+		}
+		next->next = NULL;
+		next->previous = NULL;
+	}
+
+	for (index = 0; index < countB; index++) 
+		if (preGraph->nodeReferenceMarkers[preNodeBID][index].referenceID)
+			counter++;
+
+	if (counter == 0)
+		return;
+
+	if (countA)
+		preGraph->nodeReferenceMarkers[preNodeAID] = reallocOrExitReferenceMarkers(preGraph, preNodeAID, countA + counter);
+	else
+		preGraph->nodeReferenceMarkers[preNodeAID] = callocOrExit(counter, PreMarker);
+
+	for (index = 0; index < countB; index++) {
+		markerB = &(preGraph->nodeReferenceMarkers[preNodeBID][index]);
+		if (markerB->referenceID) {
+			markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][countA++]);
+			copyPreMarker(markerA, markerB, preNodeAID, preGraph);
+			markerA->preNodeID *= -1;
+			markerA->preNodeStart = lengthB - markerA->preNodeStart - markerA->length;
+		}
+	}
+
+	preGraph->nodeReferenceMarkerCounts[preNodeAID] = countA;
+}
+
+static void concatenateReferenceMarkers_T2H_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {
+	IDnum index;
+	IDnum countA = preGraph->nodeReferenceMarkerCounts[preNodeAID];
+	IDnum countB = preGraph->nodeReferenceMarkerCounts[preNodeBID];
+	PreMarker * markerA, *next, *markerB;
+	Coordinate lengthB = preGraph->preNodes[preNodeBID].length;
+	IDnum counter = 0;
+	
+	for (index = 0 ; index < countA; index++) {
+		markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][index]);
+
+		if (markerA->preNodeID < 0)
+			next = markerA->next;
+		else 
+			next = markerA->previous;
+
+		if (!next
+		    || (markerA->preNodeID == preNodeAID && next->preNodeID != preNodeBID)
+		    || (markerA->preNodeID == -preNodeAID && next->preNodeID != -preNodeBID)) {
+			markerA->preNodeStart += lengthB;
+			continue;
+		}
+
+		next->referenceID = 0;
+		next->preNodeID = 0;
+
+		markerA->length += next->length;
+		markerA->preNodeStart = next->preNodeStart;
+		if (markerA->preNodeID < 0) {
+			markerA->next = next->next;
+			if (next->next)
+				next->next->previous = markerA;
+		} else {
+			markerA->previous = next->previous;
+			if (next->previous)
+				next->previous->next = markerA;
+			markerA->referenceStart = next->referenceStart;
+		}
+		next->next = NULL;
+		next->previous = NULL;
+	}
+
+	for (index = 0; index < countB; index++) 
+		if (preGraph->nodeReferenceMarkers[preNodeBID][index].referenceID)
+			counter++;
+
+	if (counter == 0)
+		return;
+
+	if (countA)
+		preGraph->nodeReferenceMarkers[preNodeAID] = reallocOrExitReferenceMarkers(preGraph, preNodeAID, countA + counter);
+	else
+		preGraph->nodeReferenceMarkers[preNodeAID] = callocOrExit(counter, PreMarker);
+
+	for (index = 0; index < countB; index++) {
+		markerB = &(preGraph->nodeReferenceMarkers[preNodeBID][index]);
+		if (markerB->referenceID) {
+			markerA = &(preGraph->nodeReferenceMarkers[preNodeAID][countA++]);
+			copyPreMarker(markerA, markerB, preNodeAID, preGraph);
+		}
+	}
+
+	preGraph->nodeReferenceMarkerCounts[preNodeAID] = countA;
+}
+
+void concatenateReferenceMarkers_pg(IDnum preNodeAID, IDnum preNodeBID, PreGraph * preGraph, Coordinate totalOffset) {
+	if (!referenceMarkersAreActivated_pg(preGraph))
+		return;
+
+	if (preNodeAID > 0 && preNodeBID > 0)
+		concatenateReferenceMarkers_H2T_pg(preNodeAID, preNodeBID, preGraph, totalOffset);
+	else if (preNodeAID > 0) 
+		concatenateReferenceMarkers_H2H_pg(preNodeAID, -preNodeBID, preGraph, totalOffset);
+	else if (preNodeBID > 0)
+		concatenateReferenceMarkers_T2T_pg(-preNodeAID, preNodeBID, preGraph, totalOffset);
+	else
+		concatenateReferenceMarkers_T2H_pg(-preNodeAID, -preNodeBID, preGraph, totalOffset);
+}
+
+boolean hasPreMarkers(IDnum nodeID, PreGraph * preGraph) {
+	if (nodeID < 0)
+		nodeID = -nodeID;
+	return preGraph->nodeReferenceMarkerCounts[nodeID] > 0;
+}