finishm 0.0.1

data/ext/src/src/shortReadPairs.h

@@ -0,0 +1,32 @@
+/*
+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 _SHORTREADPAIRS_H_
+#define _SHORTREADPAIRS_H_
+
+void exploitShortReadPairs(Graph * graph,
+			   ReadSet * reads,
+			   boolean * dubious,
+			   boolean * shadows,
+			   boolean force_jumps);
+void handicapNode(Node * node);
+NodeList *getMarkedNodeList();
+
+#endif

data/ext/src/src/splay.c

@@ -0,0 +1,259 @@
+/*
+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>
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#include "globals.h"
+#include "recycleBin.h"
+#include "kmer.h"
+#include "utility.h"
+
+#define CHUNKSIZE 10000
+
+static RecycleBin *treeMemory = NULL;
+
+struct splayNode_st {
+	Kmer kmer;
+	Coordinate position;
+	struct splayNode_st *left;
+	struct splayNode_st *right;
+	IDnum seqID;
+}  ATTRIBUTE_PACKED;
+
+typedef struct splayNode_st SplayNode;
+typedef struct splayNode_st SplayTree;
+
+
+#ifdef _OPENMP
+void initSplayTreeMemory(void)
+{
+	int n;
+
+	n = omp_get_max_threads();
+	#pragma omp critical
+	if (treeMemory == NULL)
+		treeMemory = newRecycleBinArray(n, sizeof(SplayNode), CHUNKSIZE);
+}
+#endif
+
+static SplayNode *allocateSplayNode()
+{
+#ifdef _OPENMP
+#ifdef DEBUG
+	if (treeMemory == NULL)
+	{
+		velvetLog("The memory for splay trees seems uninitialised, "
+			  "this is probably a bug, aborting.\n");
+		abort();
+	}
+#endif
+	return allocatePointer(getRecycleBinInArray(treeMemory,
+						    omp_get_thread_num()));
+#else
+	if (treeMemory == NULL)
+		treeMemory = newRecycleBin(sizeof(SplayNode), CHUNKSIZE);
+
+	return allocatePointer(treeMemory);
+#endif
+}
+
+void destroyAllSplayTrees()
+{
+#ifdef _OPENMP
+	destroyRecycleBinArray(treeMemory);
+#else
+	destroyRecycleBin(treeMemory);
+#endif
+	treeMemory = NULL;
+}
+
+/* This function can be called only if K2 has a left child */
+/* Perform a rotate between a node (K2) and its left child */
+/* Update heights, then return new root */
+
+static SplayNode *SingleRotateWithLeft(SplayNode * K2)
+{
+	SplayNode *K1;
+
+	K1 = K2->left;
+	K2->left = K1->right;
+	K1->right = K2;
+
+	return K1;		/* New root */
+}
+
+/* This function can be called only if K1 has a right child */
+/* Perform a rotate between a node (K1) and its right child */
+/* Update heights, then return new root */
+
+static SplayNode *SingleRotateWithRight(SplayNode * K1)
+{
+	SplayNode *K2;
+
+	K2 = K1->right;
+	K1->right = K2->left;
+	K2->left = K1;
+
+	return K2;		/* New root */
+}
+
+/* Top-down splay procedure, */
+/* not requiring kmer to be in tree */
+
+static SplayTree *Splay(Kmer * kmer, SplayTree * T)
+{
+	SplayNode Header;
+	SplayNode *LeftTreeMax, *RightTreeMin;
+
+	if (T == NULL)
+		return NULL;
+
+	Header.left = Header.right = NULL;
+	LeftTreeMax = RightTreeMin = &Header;
+
+	while (compareKmers(kmer, &(T->kmer))) {
+		if (compareKmers(kmer, &(T->kmer)) < 0) {
+			if (T->left == NULL)
+				break;
+			if (compareKmers(kmer, &(T->left->kmer)) < 0)
+				T = SingleRotateWithLeft(T);
+			if (T->left == NULL)
+				break;
+			/* Link right */
+			RightTreeMin->left = T;
+			RightTreeMin = T;
+			T = T->left;
+		} else {
+			if (T->right == NULL)
+				break;
+			if (compareKmers(kmer, &(T->right->kmer)) > 0)
+				T = SingleRotateWithRight(T);
+			if (T->right == NULL)
+				break;
+			/* Link left */
+			LeftTreeMax->right = T;
+			LeftTreeMax = T;
+			T = T->right;
+		}
+	}			/* while kmer != T->kmer */
+
+	/* Reassemble */
+	LeftTreeMax->right = T->left;
+	RightTreeMin->left = T->right;
+	T->left = Header.right;
+	T->right = Header.left;
+
+	return T;
+}
+
+Kmer * findInTree(Kmer * X, SplayTree ** T)
+{
+	*T = Splay(X, *T);
+	return &((*T)->kmer);
+}
+
+void insertIntoTree(Kmer * kmer, SplayTree ** T)
+{
+	SplayNode *newNode;
+
+	if (*T == NULL) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->left = newNode->right = NULL;
+		*T = newNode;
+		return;
+	}
+
+	*T = Splay(kmer, *T);
+	if (compareKmers(kmer, &((*T)->kmer)) < 0) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->left = (*T)->left;
+		newNode->right = *T;
+		(*T)->left = NULL;
+		*T = newNode;
+	} else if (compareKmers(&((*T)->kmer), kmer) < 0) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->right = (*T)->right;
+		newNode->left = *T;
+		(*T)->right = NULL;
+		*T = newNode;
+	}
+}
+
+boolean
+findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,
+				 Coordinate * position, SplayTree ** T)
+{
+	SplayNode *newNode;
+
+	if (*T == NULL) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->seqID = *seqID;
+		newNode->position = *position;
+
+		newNode->left = newNode->right = NULL;
+
+		*T = newNode;
+
+		return false;
+	}
+
+	*T = Splay(kmer, *T);
+	if (compareKmers(kmer, &((*T)->kmer)) < 0) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->seqID = *seqID;
+		newNode->position = *position;
+
+		newNode->left = (*T)->left;
+		newNode->right = *T;
+		(*T)->left = NULL;
+
+		*T = newNode;
+
+		return false;
+	} else if (compareKmers(kmer, &((*T)->kmer)) > 0) {
+		newNode = allocateSplayNode();
+		copyKmers(&(newNode->kmer), kmer);
+		newNode->seqID = *seqID;
+		newNode->position = *position;
+
+		newNode->right = (*T)->right;
+		newNode->left = *T;
+		(*T)->right = NULL;
+
+		*T = newNode;
+
+		return false;
+	} else {
+		*seqID = (*T)->seqID;
+		*position = (*T)->position;
+
+		return true;
+	}
+}

data/ext/src/src/splay.h

@@ -0,0 +1,43 @@
+/*
+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 _Splay_H
+#define _Splay_H
+
+#include <stdio.h>
+
+typedef struct splayNode_st SplayTree;
+
+// Deallocates tree memory
+void destroyAllSplayTrees();
+
+// Finds occurrence of kmer in the tree
+// If found, returns TRUE, and seqID and coordinate are accordingly modified
+// If not, a new leaf is added to the tree, with the seqID and position data
+boolean findOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,
+					 Coordinate * position,
+					 SplayTree ** T);
+
+#ifdef _OPENMP
+/* Initialises the per-thread RecycleBin array */
+void initSplayTreeMemory(void);
+#endif
+
+#endif

data/ext/src/src/splayTable.c

@@ -0,0 +1,1315 @@
+/*
+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 <time.h>
+#include <sys/time.h>
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#include "globals.h"
+#include "readSet.h"
+#include "splay.h"
+#include "tightString.h"
+#include "utility.h"
+#include "kmer.h"
+#include "kmerOccurenceTable.h"
+#include "recycleBin.h"
+#include "binarySequences.h"
+
+static RecycleBin * maskMemory = NULL;
+
+static Mask *allocateMask()
+{
+	if (maskMemory == NULL)
+		maskMemory = newRecycleBin(sizeof(Mask), 10000);
+
+	return (Mask *) allocatePointer(maskMemory);
+}
+
+static Mask * newMask(Coordinate position)
+{
+	Mask * mask = allocateMask();
+	mask->start = position;
+	mask->finish = position;
+	mask->next = NULL;
+	return mask;
+}
+
+// DEBUG
+boolean debug = false;
+
+#define HASH_BUCKETS_NB 16777216
+
+#ifdef _OPENMP
+
+#define NB_PUSH 32
+#define BUFFER_SIZE 4096
+
+static StringBuffer **annotationBuffer = NULL;
+static StringBuffer **annotationBufferW = NULL;
+static int *nbPush = NULL;
+static boolean producing = 1;
+
+static void initAnnotationBuffers(void)
+{
+	int n;
+	int i;
+
+	n = omp_get_max_threads();
+	annotationBuffer = callocOrExit(n, StringBuffer*);
+	annotationBufferW = callocOrExit(n, StringBuffer*);
+	nbPush = callocOrExit(n, int);
+
+	for (i = 0; i < n; i++)
+	{
+		annotationBuffer[i] = newStringBuffer(BUFFER_SIZE);
+		annotationBufferW[i] = newStringBuffer(BUFFER_SIZE);
+	}
+}
+
+static void destroyAnnotationBuffers(void)
+{
+	int n;
+	int i;
+
+	n = omp_get_max_threads();
+
+	for (i = 0; i < n; i++)
+	{
+		destroyStringBuffer(annotationBuffer[i], 1);
+		destroyStringBuffer(annotationBufferW[i], 1);
+	}
+
+	free(annotationBuffer);
+	free(annotationBufferW);
+	free(nbPush);
+	annotationBuffer = NULL;
+	annotationBufferW = NULL;
+	nbPush = NULL;
+}
+
+static void pushBufferCommit(int thread)
+{
+	StringBuffer *tmp;
+	char *s;
+
+	s = annotationBufferW[thread]->str;
+	do
+	{
+		#pragma omp flush(s)
+	}
+	while (*s);
+	tmp = annotationBufferW[thread];
+	annotationBufferW[thread] = annotationBuffer[thread];
+	annotationBuffer[thread] = tmp;
+	tmp = annotationBufferW[thread];
+	#pragma omp flush(tmp)
+}
+
+static void pushBuffer(int thread)
+{
+	if (++nbPush[thread] == NB_PUSH)
+	{
+		nbPush[thread] = 0;
+		pushBufferCommit(thread);
+	}
+}
+
+static void writeBuffers(FILE *outFile, int nbThreads)
+{
+	int i;
+
+	for (i = 0; i < nbThreads; i++)
+	{
+		StringBuffer *b;
+		char *s;
+
+		b = annotationBufferW[i];
+		#pragma omp flush(b)
+		s = b->str;
+		#pragma omp flush(s)
+		if (*s)
+		{
+			velvetFprintf(outFile, "%s", annotationBufferW[i]->str);
+			resetStringBuffer(annotationBufferW[i]);
+		}
+	}
+}
+
+static void bufferWritter(FILE *outFile)
+{
+	int n;
+
+	n = omp_get_max_threads();
+	#pragma omp flush(producing)
+	while (producing)
+	{
+		writeBuffers(outFile, n);
+		#pragma omp flush(producing)
+	}
+	writeBuffers(outFile, n);
+}
+
+static void appendLine(char *line, int thread)
+{
+	appendStringBuffer(annotationBuffer[thread], line);
+}
+#else
+
+#define BUFFER_SIZE 1024
+
+StringBuffer *annotationBuffer = NULL;
+
+static void appendLine(char *line, int thread)
+{
+	appendStringBuffer(annotationBuffer, line);
+}
+#endif
+
+struct splayTable_st {
+	SplayTree **table;
+#ifdef _OPENMP
+	omp_lock_t *tableLocks;
+#endif
+	KmerOccurenceTable *kmerOccurenceTable;
+	int WORDLENGTH;
+	boolean double_strand;
+};
+
+SplayTable *newSplayTable(int WORDLENGTH, boolean double_strand)
+{
+	SplayTable *splayTable = mallocOrExit(1, SplayTable);
+	splayTable->WORDLENGTH = WORDLENGTH;
+	splayTable->table = callocOrExit(HASH_BUCKETS_NB, SplayTree *);
+	splayTable->kmerOccurenceTable = NULL;
+	splayTable->double_strand = double_strand;
+#ifdef _OPENMP
+	splayTable->tableLocks = mallocOrExit(HASH_BUCKETS_NB, omp_lock_t);
+	int i;
+	#pragma omp parallel for
+	for (i = 0; i < HASH_BUCKETS_NB; i++)
+		omp_init_lock(splayTable->tableLocks + i);
+	initSplayTreeMemory();
+#endif
+	return splayTable;
+}
+
+void destroySplayTable(SplayTable * splayTable)
+{
+	velvetLog("Destroying splay table\n");
+
+	destroyAllSplayTrees();
+	free(splayTable->table);
+	destroyKmerOccurenceTable(splayTable->kmerOccurenceTable);
+	free(splayTable);
+
+	velvetLog("Splay table destroyed\n");
+}
+
+static KmerKey hash_kmer(Kmer * kmer)
+{
+#if KMER_LONGLONGS
+	KmerKey key = kmer->longlongs[0];
+
+#if KMER_LONGLONGS > 1
+	key ^= kmer->longlongs[1];
+#endif
+#if KMER_LONGLONGS > 2
+	key ^= kmer->longlongs[2];
+#endif
+
+	key = (~key) + (key << 21);
+	key = key ^ (key >> 24);
+	key = (key + (key << 3)) + (key << 8);
+	key = key ^ (key >> 14);
+	key = (key + (key << 2)) + (key << 4);
+	key = key ^ (key >> 28);
+	key = key + (key << 31);
+
+	return key % HASH_BUCKETS_NB;
+#elif KMER_LONGS
+	KmerKey key = kmer->longs;
+
+	key += ~(key << 15);
+	key ^= (key >> 10);
+	key += (key << 3);
+	key ^= (key >> 6);
+	key += ~(key << 11);
+	key ^= (key >> 16);
+
+	return key % HASH_BUCKETS_NB;
+
+#elif KMER_INTS
+	return kmer->ints % HASH_BUCKETS_NB;
+#elif KMER_CHARS
+	return kmer->chars % HASH_BUCKETS_NB;
+#endif
+}
+
+static Coordinate getNearestHSPIndex(Coordinate position, IDnum * sequenceIDs, Coordinate sequenceLength) {
+	Coordinate back_offset = -1;
+	Coordinate front_offset = -1;
+
+	for (back_offset = 1; position - back_offset > 0; back_offset++) 
+		if (sequenceIDs[position - back_offset])
+			break;
+
+	for (front_offset = 1; position + front_offset < sequenceLength; front_offset++) 
+		if (sequenceIDs[position + front_offset])
+			break;
+
+	if (back_offset == position && position + front_offset == sequenceLength) 
+		return -1;
+	else if (back_offset == position)
+		return position + front_offset;
+	else if (front_offset + position == sequenceLength)
+		return position - back_offset;
+	else
+		return back_offset < front_offset? position - back_offset : position + front_offset;
+}
+
+static KmerOccurence * getMostAppropriateHit(Coordinate readCoord, Coordinate readLength, boolean direct, KmerOccurence * kmerOccurence, IDnum mapCount, IDnum * mapSequenceID, Coordinate * mapCoord, int wordLength) {
+	KmerOccurence * current;
+	KmerOccurence * best = NULL;
+	Coordinate expectedPosition;
+	Coordinate positionError;
+	IDnum mapIndex;
+
+	// If only one hit
+	if (!getNextKmerOccurence(kmerOccurence))
+		return kmerOccurence;
+
+	// If multiple hits by unmapped read
+	if (mapCount == 0)
+		return NULL;
+
+	// Compare cases
+	for (current = kmerOccurence; current; current = getNextKmerOccurence(current)) {
+		for (mapIndex = 0; mapIndex < mapCount; mapIndex++) {
+
+			// If wrong sequence or unconsistent orientation	
+			if ((direct && getKmerOccurenceNodeID(current) != mapSequenceID[mapIndex]) 
+			    || (!direct && getKmerOccurenceNodeID(current) != -mapSequenceID[mapIndex])) 
+				continue;
+
+			// Compute where it is supposed to land on reference
+			if (mapSequenceID[mapIndex] < 0)
+				expectedPosition = mapCoord[mapIndex] + readLength - readCoord - 1;
+			else 
+				expectedPosition = mapCoord[mapIndex] + readCoord - wordLength + 1;
+		
+			// Compute positional error
+			positionError = getKmerOccurencePosition(current) - expectedPosition;
+
+			// If potential hit record
+			if (positionError < 1 && positionError > -1) {
+				if (best)
+					// If competing hit, give up
+					return NULL;
+				else
+					// Record current hit
+					best = current;
+			}
+		}
+	}
+
+	return best;
+}
+
+static inline boolean
+doFindOrInsertOccurenceInSplayTree(Kmer * kmer, IDnum * seqID,
+				   Coordinate * position, SplayTable *table)
+{
+#ifdef _OPENMP
+	const KmerKey kmerHash = hash_kmer(kmer);
+	boolean ret;
+
+	omp_set_lock(table->tableLocks + kmerHash);
+	ret =  findOrInsertOccurenceInSplayTree(kmer, seqID, position,
+						table->table + kmerHash);
+	omp_unset_lock(table->tableLocks + kmerHash);
+
+	return ret;
+#else
+	return findOrInsertOccurenceInSplayTree(kmer, seqID, position,
+						&table->table[hash_kmer(kmer)]);
+#endif
+}
+
+
+static boolean findOrInsertOccurenceInSplayTable(Kmer * kmer, IDnum * seqID,
+						 Coordinate * position,
+						 SplayTable * table, IDnum * sequenceIDs,
+						 Coordinate * coords, Coordinate readIndex, Coordinate readLength, boolean direct)
+{
+	KmerOccurence * hit;
+	Coordinate HSPIndex;
+
+	// Check if previous anchor
+	if (sequenceIDs && sequenceIDs[readIndex]) {
+		if (direct)
+			*seqID = sequenceIDs[readIndex];
+		else 
+			*seqID = -sequenceIDs[readIndex];
+		if (sequenceIDs[readIndex] > 0) 
+			*position = coords[readIndex] + readIndex;
+		else
+			*position = coords[readIndex] - readIndex + readLength - 1;
+
+		return true;
+	}
+	else if (coords && coords[readIndex]) 
+		// If in buffer zone:
+		return doFindOrInsertOccurenceInSplayTree(kmer, seqID, position, table);
+
+
+	if (debug)
+		abort();
+	// Look up first in reference sequence k-mers
+	if (table->kmerOccurenceTable 
+	    && (hit = findKmerInKmerOccurenceTable(kmer, table->kmerOccurenceTable))) {
+		if (!getNextKmerOccurence(hit)) {
+			*seqID = getKmerOccurenceNodeID(hit);
+			*position = getKmerOccurencePosition(hit);
+			return true;
+		} else if ((HSPIndex = getNearestHSPIndex(*position, sequenceIDs, readLength)) > 0) {
+	    		hit = getMostAppropriateHit(readIndex, readLength, direct, hit, 1, &(sequenceIDs[HSPIndex]), &(coords[HSPIndex]), table->WORDLENGTH);
+			if (hit) {
+				*seqID = getKmerOccurenceNodeID(hit);
+				*position = getKmerOccurencePosition(hit);
+				return true;
+			}
+
+		}
+	} 
+
+	// If not, go through the novel k-mers
+	return doFindOrInsertOccurenceInSplayTree(kmer, seqID, position, table);
+}
+
+static void printAnnotations(IDnum *sequenceIDs, Coordinate * coords,
+			     TightString * array, SplayTable * table,
+			     FILE * file, boolean second_in_pair, IDnum seqID) 
+{
+	Coordinate readNucleotideIndex = 0;
+	Coordinate writeNucleotideIndex = 0;
+	Kmer word;
+	Kmer antiWord;
+	boolean annotationClosed = true;
+	IDnum sequenceID;
+	Coordinate coord;
+	boolean found;
+	Coordinate position = 0;
+	Coordinate start = 0;
+	Coordinate finish = 0;
+	IDnum referenceSequenceID = 0;
+	Nucleotide nucleotide;
+	char lineBuffer[MAXLINE];
+	TightString * tString = getTightStringInArray(array, seqID - 1); 
+	int thread = 0;
+
+	clearKmer(&word);
+	clearKmer(&antiWord);
+
+#ifdef _OPENMP
+	thread = omp_get_thread_num();
+#endif
+
+	if (debug) 
+		abort();
+
+	sprintf(lineBuffer, "ROADMAP %li\n", (long)seqID);
+	appendLine(lineBuffer, thread);
+
+	// Neglect any string shorter than WORDLENGTH :
+	if (getLength(tString) < table->WORDLENGTH) {
+#ifdef _OPENMP
+		pushBuffer(thread);
+#else
+		velvetFprintf(file, "%s", annotationBuffer->str);
+		resetStringBuffer(annotationBuffer);
+#endif
+		return;
+	}
+
+	// Fill in the initial word : 
+	for (readNucleotideIndex = 0;
+	     readNucleotideIndex < table->WORDLENGTH - 1;
+	     readNucleotideIndex++) { 
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+#ifdef COLOR
+		reversePushNucleotide(&antiWord, nucleotide);
+#else
+		reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+	}
+
+	while (readNucleotideIndex < getLength(tString)) {
+		// Shift word:
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+#ifdef COLOR
+		reversePushNucleotide(&antiWord, nucleotide);
+#else
+		reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+
+		sequenceID = seqID;
+		coord = writeNucleotideIndex;
+
+		if (table->double_strand) {
+			if (compareKmers(&word, &antiWord) <= 0) {
+				found =
+				    findOrInsertOccurenceInSplayTable(&word,
+								      &sequenceID,
+								      &coord,
+								      table,
+								      sequenceIDs, 
+								      coords,
+								      readNucleotideIndex,
+								      getLength(tString),
+								      true);
+			} else {
+				sequenceID = -sequenceID;
+				found =
+				    findOrInsertOccurenceInSplayTable(&antiWord,
+								      &sequenceID,
+								      &coord,
+								      table, 
+								      sequenceIDs, 
+								      coords,
+								      readNucleotideIndex,
+								      getLength(tString),
+								      false);
+				sequenceID = -sequenceID;
+			}
+		} else {
+			if (!second_in_pair) {
+				found =
+				    findOrInsertOccurenceInSplayTable(&word,
+								      &sequenceID,
+								      &coord,
+								      table,
+								      sequenceIDs, 
+								      coords,
+								      readNucleotideIndex,
+								      getLength(tString),
+								      true);
+			} else {
+				sequenceID = -sequenceID;
+				found =
+				    findOrInsertOccurenceInSplayTable(&antiWord,
+								      &sequenceID,
+								      &coord,
+								      table, 
+								      sequenceIDs, 
+								      coords,
+								      readNucleotideIndex,
+								      getLength(tString),
+								      false);
+				sequenceID = -sequenceID;
+			}
+		}
+
+		if (!found) {
+			writeNucleotideIndex++;
+			if (!annotationClosed) {
+				sprintf(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
+					(long) referenceSequenceID, (long long) position,
+					(long long) start, (long long) finish);
+				appendLine(lineBuffer, thread);
+			}
+			annotationClosed = true;
+		}
+		// Otherwise create/complete annotation:
+		else {
+			// Forbidden k-mer
+			if (sequenceID == 0) {
+				break;
+			}
+			// Closed/inexistant annotation
+			else if (annotationClosed) {
+				referenceSequenceID = sequenceID;
+				position = writeNucleotideIndex;
+				start = finish = coord;
+
+				if (referenceSequenceID > 0)
+					finish++;
+				else
+					finish--;
+
+				annotationClosed = false;
+			}
+			// Open annotation
+			else if (sequenceID == referenceSequenceID
+				 && coord == finish) {
+				if (referenceSequenceID > 0)
+					finish++;
+				else
+					finish--;
+			}
+			// Previous non corresponding annotation
+			else {
+				sprintf(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
+					(long) referenceSequenceID, (long long) position,
+					(long long) start, (long long) finish);
+				appendLine(lineBuffer, thread);
+
+				referenceSequenceID = sequenceID;
+				position = writeNucleotideIndex;
+				start = finish = coord;
+
+				if (referenceSequenceID > 0)
+					finish++;
+				else
+					finish--;
+			}
+		}
+
+		readNucleotideIndex++;
+	}
+
+	if (!annotationClosed) {
+		sprintf(lineBuffer, "%ld\t%lld\t%lld\t%lld\n",
+			(long) referenceSequenceID, (long long) position,
+			(long long) start, (long long) finish);
+		appendLine(lineBuffer, thread);
+	}
+#ifdef _OPENMP
+	pushBuffer(thread);
+#else
+	velvetFprintf(file, "%s", annotationBuffer->str);
+	resetStringBuffer(annotationBuffer);
+#endif
+
+	return;
+}
+
+static void computeClearHSPs(TightString * array, boolean second_in_pair, SplayTable * table, IDnum ** sequenceIDs, Coordinate ** coords, IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount, IDnum seqID) {
+	Coordinate readNucleotideIndex = 0;
+	Kmer word;
+	Kmer antiWord;
+	Kmer polyA;
+	Nucleotide nucleotide;
+	KmerOccurence * hit;
+
+	int penalty;
+	TightString * tString;
+	Coordinate length;
+
+	clearKmer(&polyA);
+	tString = getTightStringInArray(array, seqID - 1);
+	length = getLength(tString);
+	*sequenceIDs = callocOrExit(length, IDnum);
+	*coords = callocOrExit(length, Coordinate);
+
+	// First pass for unambiguous hits
+	// Fill in the initial word : 
+	clearKmer(&word);
+	clearKmer(&antiWord);
+	for (readNucleotideIndex = 0;
+	     readNucleotideIndex < table->WORDLENGTH - 1;
+	     readNucleotideIndex++) { 
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+#ifdef COLOR
+		reversePushNucleotide(&antiWord, nucleotide);
+#else
+		reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+	}
+
+	// Kill silly poly-T beginnings
+	while (readNucleotideIndex < getLength(tString) && (compareKmers(&antiWord, &polyA) == 0 || compareKmers(&word, &polyA) == 0)) {
+		nucleotide = getNucleotide(readNucleotideIndex++, tString);
+		pushNucleotide(&word, nucleotide);
+#ifdef COLOR
+		reversePushNucleotide(&antiWord, nucleotide);
+#else
+		reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+	}
+
+	while (readNucleotideIndex < getLength(tString)) {
+		// Shift word:
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+
+#ifdef COLOR
+		reversePushNucleotide(&antiWord, nucleotide);
+#else
+		reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+
+		if (table->double_strand) {
+			if (compareKmers(&word, &antiWord) <= 0) {
+				hit = findKmerInKmerOccurenceTable(&word, table->kmerOccurenceTable); 
+
+				if (hit && (hit = getMostAppropriateHit(readNucleotideIndex, getLength(tString), true, hit, mapCount, mapReferenceIDs, mapCoords, table->WORDLENGTH))) 
+					(*sequenceIDs)[readNucleotideIndex] = getKmerOccurenceNodeID(hit);
+			} else {
+				hit = findKmerInKmerOccurenceTable(&antiWord, table->kmerOccurenceTable); 
+
+				if (hit && (hit = getMostAppropriateHit(readNucleotideIndex, getLength(tString), false, hit, mapCount, mapReferenceIDs, mapCoords, table->WORDLENGTH))) 
+					(*sequenceIDs)[readNucleotideIndex] = -getKmerOccurenceNodeID(hit);
+			}
+		} else {
+			if (!second_in_pair) {
+				hit = findKmerInKmerOccurenceTable(&word, table->kmerOccurenceTable); 
+
+				if (hit && (hit = getMostAppropriateHit(readNucleotideIndex, getLength(tString), true, hit, mapCount, mapReferenceIDs, mapCoords, table->WORDLENGTH))) 
+					(*sequenceIDs)[readNucleotideIndex] = getKmerOccurenceNodeID(hit);
+			} else {
+				hit = findKmerInKmerOccurenceTable(&antiWord, table->kmerOccurenceTable); 
+
+				if (hit && (hit = getMostAppropriateHit(readNucleotideIndex, getLength(tString), false, hit, mapCount, mapReferenceIDs, mapCoords, table->WORDLENGTH))) 
+					(*sequenceIDs)[readNucleotideIndex] = -getKmerOccurenceNodeID(hit);
+			}
+		}
+
+		if ((*sequenceIDs)[readNucleotideIndex]) {
+			if ((*sequenceIDs)[readNucleotideIndex] > 0) 
+				(*coords)[readNucleotideIndex] = getKmerOccurencePosition(hit) - readNucleotideIndex;
+			else
+				(*coords)[readNucleotideIndex] = getKmerOccurencePosition(hit) + readNucleotideIndex - getLength(tString) + 1;
+		}
+	
+		// Barrier to flip-flopping
+		if ((*sequenceIDs)[readNucleotideIndex - 1] != 0
+		    && ((*sequenceIDs)[readNucleotideIndex] != (*sequenceIDs)[readNucleotideIndex - 1]
+			|| (*coords)[readNucleotideIndex] != (*coords)[readNucleotideIndex - 1])) {
+			// Break in continuity... skip k positions 
+			(*sequenceIDs)[readNucleotideIndex] = 0;
+			(*coords)[readNucleotideIndex] = -1;
+			readNucleotideIndex++;
+
+			for (penalty = 0; penalty < table->WORDLENGTH  - 1 && readNucleotideIndex < getLength(tString); penalty++) {
+				nucleotide = getNucleotide(readNucleotideIndex, tString);
+				pushNucleotide(&word, nucleotide);
+
+#ifdef COLOR
+				reversePushNucleotide(&antiWord, nucleotide);
+#else
+				reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+				(*sequenceIDs)[readNucleotideIndex] = 0;
+				(*coords)[readNucleotideIndex] = -1;
+				readNucleotideIndex++;
+			}
+		} else
+			readNucleotideIndex++;
+		
+	}
+
+	free(mapReferenceIDs);
+	free(mapCoords);
+}
+
+void inputSequenceIntoSplayTable(TightString * array,
+				 SplayTable * table,
+				 FILE * file,
+				 boolean second_in_pair,
+				 IDnum * mapReferenceIDs, Coordinate * mapCoords, Coordinate mapCount,
+				 IDnum seqID)
+{
+	IDnum * sequenceIDs = NULL;
+	Coordinate * coords = NULL;
+
+	//debug = (seqID == 29405);
+
+	// If appropriate, get the HSPs on reference sequences
+	if (table->kmerOccurenceTable) 
+		computeClearHSPs(array, second_in_pair, table, &sequenceIDs, &coords, mapReferenceIDs, mapCoords, mapCount, seqID);
+
+	// Go through read, eventually with annotations
+	printAnnotations(sequenceIDs, coords, array, table, file, second_in_pair, seqID);
+
+	// Clean up
+	if (sequenceIDs) {
+		free(sequenceIDs);
+		free(coords);
+	}
+}
+
+void inputReferenceIntoSplayTable(TightString * tString,
+				 SplayTable * table, FILE * file, IDnum seqID, Mask * mask)
+{
+	IDnum currentIndex;
+	Coordinate readNucleotideIndex = 0;
+	Coordinate kmerIndex = 0;
+	Kmer word;
+	Kmer antiWord;
+	Nucleotide nucleotide;
+	Mask * currentMask = mask;
+#ifdef _OPENMP
+	char lineBuffer[MAXLINE];
+#endif
+
+	clearKmer(&word);
+	clearKmer(&antiWord);
+
+	currentIndex = seqID;
+#ifdef _OPENMP
+	sprintf(lineBuffer, "ROADMAP %li\n", (long)currentIndex);
+	appendLine(lineBuffer, omp_get_thread_num());
+#else
+	velvetFprintf(file, "ROADMAP %li\n", (long)currentIndex);
+#endif
+
+	// Neglect any string shorter than WORDLENGTH :
+	if (getLength(tString) < table->WORDLENGTH) {
+		return;
+	}
+
+	// Fill in the initial word : 
+	for (readNucleotideIndex = 0;
+	     readNucleotideIndex < table->WORDLENGTH - 1;
+	     readNucleotideIndex++) { 
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+		if (table->double_strand) {
+#ifdef COLOR
+			reversePushNucleotide(&antiWord, nucleotide);
+#else
+			reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+		}
+	}
+
+	while (readNucleotideIndex < getLength(tString)) {
+		// Shift word:
+		nucleotide = getNucleotide(readNucleotideIndex, tString);
+		pushNucleotide(&word, nucleotide);
+
+		if (table->double_strand) {
+#ifdef COLOR
+			reversePushNucleotide(&antiWord, nucleotide);
+#else
+			reversePushNucleotide(&antiWord, 3 - nucleotide);
+#endif
+		}
+
+		// Check for gap masks:
+		if (currentMask && currentMask->start - table->WORDLENGTH + 1 <= readNucleotideIndex) {
+			while(currentMask && currentMask->finish + table->WORDLENGTH - 1 < readNucleotideIndex)
+				currentMask = currentMask->next;
+
+			if (currentMask && currentMask->finish + table->WORDLENGTH - 1 >= readNucleotideIndex) {
+				readNucleotideIndex++;
+				kmerIndex++;
+				continue;
+			}
+		}
+
+		// Record k-mer
+		if (table->double_strand) {
+			if (compareKmers(&word, &antiWord) <= 0)
+				recordKmerOccurence(&word, currentIndex, 
+						    kmerIndex,
+						    table->kmerOccurenceTable);
+			else
+				recordKmerOccurence(&antiWord, -currentIndex, 
+							kmerIndex,
+							table->kmerOccurenceTable);
+		} else {
+			recordKmerOccurence(&word, currentIndex, 
+					    kmerIndex,
+					    table->kmerOccurenceTable);
+		}
+		readNucleotideIndex++;
+		kmerIndex++;
+	}
+
+	return;
+}
+
+static Coordinate countReferenceKmers(ReadSet * reads, int wordLength) {
+	IDnum readIndex;
+	Coordinate length = 0;
+	
+
+	for (readIndex = 0; readIndex < reads->readCount && reads->categories[readIndex] == REFERENCE; readIndex++)	
+	{
+		Coordinate tmpLength = getLength(getTightStringInArray(reads->tSequences, readIndex));
+		if (tmpLength >= wordLength)
+			length += tmpLength - wordLength + 1;
+	}
+
+	return length;
+}
+
+Mask ** scanReferenceSequences(FILE * file, IDnum referenceSequenceCount) {
+	Mask ** referenceMasks = callocOrExit(referenceSequenceCount, Mask*);
+	IDnum index;
+	char line[MAXLINE];
+	char c = '\0';
+
+	// Search sequences for masks
+	for (index = 0; index < referenceSequenceCount; index++) {
+		Mask * current = NULL;
+		Coordinate position = 0;
+		boolean openMask = false;
+
+		// Read through header
+		fgets(line, MAXLINE, file);
+
+		// Read through sequence
+		while ((c = getc(file))) {
+			if (c == EOF || c == '>')
+				break;
+			else if (c == '\r' || c == '\n')
+				continue;
+			else if (c == 'n' || c == 'N') {
+				if (openMask)
+					current->finish++;
+				else if (referenceMasks[index] == NULL) {
+					referenceMasks[index] = newMask(position);
+					current = referenceMasks[index];
+				} else {
+					current->next = newMask(position);
+					current = current->next;		
+				}
+				openMask = true;
+				position++;
+			} else {
+				openMask = false;
+				position++;
+			}
+		}
+	}
+
+	if (c != '\0')
+		ungetc(c, file);
+	return referenceMasks;
+}
+
+Mask ** scanBinaryReferenceSequences(SequencesReader *seqReadInfo, IDnum referenceSequenceCount) {
+	Mask ** referenceMasks = callocOrExit(referenceSequenceCount, Mask*);
+	IDnum index;
+	char line[MAXLINE];
+	char c = '\0';
+	FILE *file = fopen(seqReadInfo->m_namesFilename, "r");
+	if (file == NULL) {
+		exitErrorf(EXIT_FAILURE, true, "Couldn't read file %s", seqReadInfo->m_namesFilename);
+	} else {
+		velvetLog("Reading mapping info from %s\n", seqReadInfo->m_namesFilename);
+	}
+
+	// Search sequences for masks
+	for (index = 0; index < referenceSequenceCount; index++) {
+		Mask * current = NULL;
+		long start = 0;
+		long finish = 0;
+		long number;
+		long cat;
+
+		// Read through header
+		if ((c = getc(file)) != '>') {
+			exitErrorf(EXIT_FAILURE, false, "names line did not start with >");
+		}
+		fgets(line, MAXLINE, file);
+		sscanf(line, "%*[^\t]\t%li\t%li\n", &number, &cat);
+		// ensure is is a ref cat
+		if ((IDnum) number != index + 1) {
+			exitErrorf(EXIT_FAILURE, false, "sequence %ld != expected %ld", number, (long) index);
+		}
+		if ((Category) cat != REFERENCE) {
+			exitErrorf(EXIT_FAILURE, false, "unexpected category %ld", cat);
+		}
+
+		// Read through the reference maps
+		while ((c = getc(file))) {
+			if (c == EOF || c == '>') {
+				break;
+			}
+			ungetc(c, file);
+			fgets(line, MAXLINE, file);
+			sscanf(line, "%li\t%li\n", &start, &finish);
+			if (referenceMasks[index] == NULL) {
+				referenceMasks[index] = newMask(start);
+				referenceMasks[index]->finish = finish;
+				current = referenceMasks[index];
+			} else {
+				current->next = newMask(start);
+				current->next->finish = finish;
+				current = current->next;		
+			}
+		}
+		ungetc(c, file);
+	}
+
+	fclose(file);
+	return referenceMasks;
+}
+
+void inputSequenceArrayIntoSplayTableAndArchive(ReadSet * reads,
+						SplayTable * table,
+						char *filename, char* seqFilename)
+{
+	IDnum index;
+	IDnum sequenceCount = reads->readCount;
+	TightString *array;
+	FILE *outfile = fopen(filename, "w");
+	FILE *seqFile = NULL;
+	IDnum kmerCount;
+	IDnum referenceSequenceCount = 0;
+	struct timeval start, end, diff;
+	SequencesReader seqReadInfo;
+	memset(&seqReadInfo, 0, sizeof(seqReadInfo));
+	if (isCreateBinary()) {
+		seqReadInfo.m_bIsBinary = true;
+		seqReadInfo.m_pFile = openCnySeqForRead(seqFilename, &seqReadInfo.m_unifiedSeqFileHeader);
+		if (!seqReadInfo.m_pFile) {
+			exitErrorf(EXIT_FAILURE, true, "Could not open %s", seqFilename);
+		}
+		seqReadInfo.m_namesFilename = mallocOrExit(strlen(seqFilename) + sizeof(".names"), char);
+		sprintf(seqReadInfo.m_namesFilename, "%s.names", seqFilename);
+		seqReadInfo.m_numCategories = seqReadInfo.m_unifiedSeqFileHeader.m_numCategories;
+		seqReadInfo.m_minSeqLen = seqReadInfo.m_unifiedSeqFileHeader.m_minSeqLen;
+		seqReadInfo.m_maxSeqLen = seqReadInfo.m_unifiedSeqFileHeader.m_maxSeqLen;
+		seqReadInfo.m_bIsRef = false;
+		seqReadInfo.m_pReadBuffer = mallocOrExit(USF_READ_BUF_SIZE, uint8_t );
+		seqReadInfo.m_pCurrentReadPtr = seqReadInfo.m_pReadBufEnd = 0;
+
+		resetCnySeqCurrentRead(&seqReadInfo);
+	} else {
+		seqReadInfo.m_bIsBinary = false;
+	}
+	IDnum ** mapReferenceIDs = NULL;
+	Coordinate ** mapCoords = NULL;
+	Coordinate * mapCount = NULL;
+
+	char line[MAXLINE];
+	char c;
+	IDnum seqID = 0;
+	long long_var;
+	long long longlong_var;
+	Coordinate maxCount = 20;
+	Coordinate counter = 0;
+	// DEBUG 
+	Mask ** referenceMasks = NULL;
+
+	if (outfile == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Couldn't write to file %s", filename);
+	else
+		velvetLog("Writing into roadmap file %s...\n", filename);
+
+	// Count reference sequences
+	for (index = 0; index < reads->readCount && reads->categories[index] == REFERENCE; index++)
+		referenceSequenceCount++;
+
+	velvetFprintf(outfile, "%ld\t%ld\t%i\t%hi\n", (long) sequenceCount, (long) referenceSequenceCount, table->WORDLENGTH, (short) table->double_strand);
+
+	if (reads->tSequences == NULL)
+		convertSequences(reads);
+
+	gettimeofday(&start, NULL);
+	array = reads->tSequences;
+
+#ifdef _OPENMP
+	if (omp_get_max_threads() == 1)
+	{
+		omp_set_num_threads(2);
+		omp_set_nested(0);
+	}
+	else
+		omp_set_nested(1);
+	initAnnotationBuffers();
+#else
+	annotationBuffer = newStringBuffer(BUFFER_SIZE);
+#endif
+
+	if (referenceSequenceCount && (kmerCount = countReferenceKmers(reads, table->WORDLENGTH)) > 0) {
+		table->kmerOccurenceTable = newKmerOccurenceTable(24 , table->WORDLENGTH);
+		allocateKmerOccurences(kmerCount, table->kmerOccurenceTable);
+		if (seqReadInfo.m_bIsBinary) {
+			referenceMasks = scanBinaryReferenceSequences(&seqReadInfo, referenceSequenceCount);
+			// binary seqs have no Ns so just advance past the references
+			for (index = 0; index < referenceSequenceCount; index++) {
+				TightString cmpString;
+				cmpString.length = seqReadInfo.m_currentReadLength;
+				cmpString.sequence = mallocOrExit((seqReadInfo.m_currentReadLength + 3) / 4, uint8_t );
+				getCnySeqNucl(&seqReadInfo, cmpString.sequence);
+				if (seqReadInfo.m_bIsRef) {
+					seqReadInfo.m_refCnt = readCnySeqUint32(&seqReadInfo);
+					// now the next ptr is advanced
+					seqReadInfo.m_pNextReadPtr += (sizeof(RefInfo) * seqReadInfo.m_refCnt);
+					RefInfo refElem;
+					uint32_t refIdx;
+					for (refIdx = 0; refIdx < seqReadInfo.m_refCnt; refIdx++) {
+						// not actually used so just read past refs
+						refElem.m_referenceID = readCnySeqUint32(&seqReadInfo);
+						refElem.m_pos = readCnySeqUint32(&seqReadInfo);
+					}
+				}
+				// optional test to ensure reference mapping seqIDs are in sync
+#if 0
+				TightString *tString;
+				tString = getTightStringInArray(array, index);
+				if (getLength(tString) != seqReadInfo.m_currentReadLength) {
+					velvetLog("Error: TightString len mismatch, %d != %ld\n", getLength(tString), seqReadInfo.m_currentReadLength);
+					exit(1);
+				}
+				char *str = readTightString(tString);
+				char *cmpStr = readTightString(&cmpString);
+				if (strcmp(str, cmpStr) != 0) {
+					printf("seq %s != cmp %s\n", str, cmpStr);
+					exit(1);
+				}
+				free(str);
+				free(cmpStr);
+#endif
+				advanceCnySeqCurrentRead(&seqReadInfo);
+				free(cmpString.sequence);
+			}
+		} else {
+			seqFile = fopen(seqFilename, "r");
+
+			if (seqFile == NULL)
+				exitErrorf(EXIT_FAILURE, true, "Couldn't write to file %s", seqFilename);
+			else
+				velvetLog("Reading mapping info from file %s\n", seqFilename);
+
+			seqReadInfo.m_pFile = seqFile;
+
+			// Skip through reference headers quickly
+			referenceMasks = scanReferenceSequences(seqFile, referenceSequenceCount);
+		}
+
+#ifdef _OPENMP
+		producing = 1;
+		#pragma omp parallel sections
+		{
+			#pragma omp section
+			{
+				bufferWritter(outfile);
+			}
+			#pragma omp section
+			{
+				#pragma omp parallel for
+#endif
+				for (index = 0; index < referenceSequenceCount; index++)
+					inputReferenceIntoSplayTable(getTightStringInArray(array, index),
+								     table, outfile, index + 1, referenceMasks[index]);
+
+#ifdef _OPENMP
+				for (index = omp_get_max_threads() - 1; index >= 0; index--)
+					pushBufferCommit(index);
+				producing = 0;
+				#pragma omp flush(producing)
+			}
+		}
+#endif
+
+		if (maskMemory)
+			destroyRecycleBin(maskMemory);
+		maskMemory = NULL;
+		sortKmerOccurenceTable(table->kmerOccurenceTable);
+	}
+
+	velvetLog("Inputting sequences...\n");
+
+	if (table->kmerOccurenceTable) {
+		mapReferenceIDs = callocOrExit(sequenceCount + 1, IDnum*);
+		mapCoords = callocOrExit(sequenceCount + 1, Coordinate *);
+		mapCount = callocOrExit(sequenceCount + 1, Coordinate);
+
+		RefInfo *refArray = NULL;
+		if (seqReadInfo.m_bIsBinary) {
+			TightString cmpString;
+			for (seqID = referenceSequenceCount + 1; seqID < sequenceCount + 1; seqID++) {
+				cmpString.length = seqReadInfo.m_currentReadLength;
+				cmpString.sequence = mallocOrExit((seqReadInfo.m_currentReadLength + 3) / 4, uint8_t );
+				getCnySeqNucl(&seqReadInfo, cmpString.sequence);
+				if (seqReadInfo.m_bIsRef) {
+					seqReadInfo.m_refCnt = readCnySeqUint32(&seqReadInfo);
+					// now the next ptr is advanced
+					seqReadInfo.m_pNextReadPtr += (sizeof(RefInfo) * seqReadInfo.m_refCnt);
+					refArray = callocOrExit(seqReadInfo.m_refCnt, RefInfo);
+					uint32_t refIdx;
+					for (refIdx = 0; refIdx < seqReadInfo.m_refCnt; refIdx++) {
+						refArray[refIdx].m_referenceID = readCnySeqUint32(&seqReadInfo);
+						refArray[refIdx].m_pos = readCnySeqUint32(&seqReadInfo);
+					}
+				}
+				// optional test to ensure reference mapping seqIDs are in sync
+#if 0
+				TightString *tString;
+				tString = getTightStringInArray(array, seqID - 1);
+				if (getLength(tString) != seqReadInfo.m_currentReadLength) {
+					velvetLog("Error: TightString len mismatch, %d != %ld\n", getLength(tString), seqReadInfo.m_currentReadLength);
+					exit(1);
+				}
+				char *str = readTightString(tString);
+				char *cmpStr = readTightString(&cmpString);
+				if (strcmp(str, cmpStr) != 0) {
+					printf("seq %s != cmp %s\n", str, cmpStr);
+					exit(1);
+				}
+				free(str);
+				free(cmpStr);
+#endif
+				free(cmpString.sequence);
+
+				// set prior count
+				mapCount[seqID - 1] = counter;
+				counter = 0;
+				maxCount = 20;
+				mapReferenceIDs[seqID] = callocOrExit(maxCount, IDnum);
+				mapCoords[seqID] = callocOrExit(maxCount, Coordinate);
+
+				if (seqReadInfo.m_bIsRef) {
+					while (counter < seqReadInfo.m_refCnt) {
+						mapReferenceIDs[seqID][counter] = (IDnum) refArray[counter].m_referenceID;
+						mapCoords[seqID][counter] = (Coordinate) refArray[counter].m_pos;
+
+						if (++counter == maxCount) {
+							maxCount *= 2;
+							mapReferenceIDs[seqID] = reallocOrExit(mapReferenceIDs[seqID], maxCount, IDnum);
+							mapCoords[seqID] = reallocOrExit(mapCoords[seqID], maxCount, Coordinate);
+						}
+					}
+					free(refArray);
+				}
+				advanceCnySeqCurrentRead(&seqReadInfo);
+			}
+		} else {
+			// Parse file for mapping info
+			while (seqFile && (c = getc(seqFile)) != EOF) {
+
+				if (c == '>') {
+					mapCount[seqID] = counter;
+					counter = 0;
+					maxCount = 20;
+					fgets(line, MAXLINE, seqFile);
+					sscanf(line,"%*[^\t]\t%li\t", &long_var);
+					seqID = (IDnum) long_var;
+					mapReferenceIDs[seqID] = callocOrExit(maxCount, IDnum);
+					mapCoords[seqID] = callocOrExit(maxCount, Coordinate);
+				} else if (c == 'M') {
+					fgets(line, MAXLINE, seqFile);
+					sscanf(line,"\t%li\t%lli\n", &long_var, &longlong_var);
+					mapReferenceIDs[seqID][counter] = (IDnum) long_var;
+					mapCoords[seqID][counter] = (Coordinate) longlong_var;
+
+					if (++counter == maxCount) {
+						maxCount *= 2;
+						mapReferenceIDs[seqID] = reallocOrExit(mapReferenceIDs[seqID], maxCount, IDnum);
+						mapCoords[seqID] = reallocOrExit(mapCoords[seqID], maxCount, Coordinate);
+					}
+				}
+			}
+		}
+	}
+	if (seqFile)
+		fclose(seqFile);
+
+	if (seqReadInfo.m_bIsBinary) {
+		if (seqReadInfo.m_pReadBuffer) {
+			free(seqReadInfo.m_pReadBuffer);
+		}
+		fclose(seqReadInfo.m_pFile);
+	}
+
+#ifdef _OPENMP
+	producing = 1;
+	#pragma omp parallel sections
+	{
+		#pragma omp section
+		{
+			bufferWritter(outfile);
+		}
+		#pragma omp section
+		{
+			#pragma omp parallel for
+#endif
+			for (index = referenceSequenceCount; index < sequenceCount; index++)
+			{
+				boolean second_in_pair;
+
+				// Progress report on screen
+				if (index % 1000000 == 0) {
+					velvetLog("Inputting sequence %li / %li\n",
+						  (long)index, (long)sequenceCount);
+					fflush(stdout);
+				}
+
+				// Test to make sure that all the reference reads are before all the other reads
+				if (reads->categories[index] == REFERENCE) {
+					velvetLog("Reference sequence placed after a non-reference read!\n");
+					velvetLog(">> Please re-order the filenames in your command line so as "
+						  "to have the reference sequence files before all the others\n");
+#ifdef DEBUG 
+					abort();
+#endif 
+					exit(0);
+				}
+				second_in_pair = reads->categories[index] % 2 && isSecondInPair(reads, index);
+
+				// Hashing the reads
+				if (table->kmerOccurenceTable)
+				    inputSequenceIntoSplayTable(array, table,
+								outfile,
+								second_in_pair, mapReferenceIDs[index + 1], mapCoords[index+1], mapCount[index+1], index + 1);
+				else
+				    inputSequenceIntoSplayTable(array, table,
+								outfile,
+								second_in_pair, NULL, NULL, 0, index + 1);
+			}
+#ifdef _OPENMP
+			for (index = omp_get_max_threads() - 1; index >= 0; index--)
+				pushBufferCommit(index);
+			producing = 0;
+			#pragma omp flush(producing)
+		}
+	}
+	destroyAnnotationBuffers();
+#else
+	destroyStringBuffer(annotationBuffer, 1);
+#endif
+
+	gettimeofday(&end, NULL);
+	timersub(&end, &start, &diff);
+	velvetLog(" === Sequences loaded in %ld.%06ld s\n", (long) diff.tv_sec, (long) diff.tv_usec);
+
+	fclose(outfile);
+
+	if (mapReferenceIDs) {
+		free(mapReferenceIDs);
+		free(mapCoords);
+		free(mapCount);
+	}
+	if (referenceMasks) {
+		free(referenceMasks);
+	}
+	if (seqReadInfo.m_namesFilename) {
+		free(seqReadInfo.m_namesFilename);
+	}
+	//free(reads->tSequences);
+	//reads->tSequences = NULL;
+	//destroyReadSet(reads);
+	velvetLog("Done inputting sequences\n");
+}