finishm 0.0.1

data/ext/src/src/readCoherentGraph.h

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

data/ext/src/src/readSet.c

@@ -0,0 +1,1734 @@
+/*
+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 <math.h>
+#include <time.h>
+#include <limits.h>
+#include <ctype.h>
+
+#include "globals.h"
+#include "tightString.h"
+#include "readSet.h"
+#include "utility.h"
+#include "binarySequences.h"
+#include "autoOpen.h"
+#include "kseq.h"
+
+#if !defined(BUNDLEDZLIB)
+#include <zlib.h>
+#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+#else
+#include "../third-party/zlib-1.2.3/zlib.h"
+#endif
+
+#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+#  include <fcntl.h>
+#  include <io.h>
+#  define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
+#else
+#  define SET_BINARY_MODE(file)
+#endif
+
+static Mask *allocateMask(SequencesWriter *seqWriteInfo)
+{
+	if (seqWriteInfo->m_maskMemory == NULL)
+		seqWriteInfo->m_maskMemory = newRecycleBin(sizeof(Mask), 10000);
+
+	return (Mask *) allocatePointer(seqWriteInfo->m_maskMemory);
+}
+
+static Mask * newMask(SequencesWriter *seqWriteInfo, Coordinate position)
+{
+	Mask * mask = allocateMask(seqWriteInfo);
+	mask->start = position;
+	mask->finish = position;
+	mask->next = NULL;
+	return mask;
+}
+
+//
+// cmd line args can override the createBinary flag
+// note that createBinary is only used by velveth
+//
+boolean createBinary = false;
+boolean isCreateBinary()
+{
+	return createBinary;
+}
+
+void setCreateBinary(boolean val)
+{
+	createBinary = val;
+}
+
+ReadSet *newReadSet()
+{
+	ReadSet *rs = callocOrExit(1, ReadSet);
+	return rs;
+}
+
+//////////////////////////////////////////////////////////////////////////
+// Reference identifiers
+//////////////////////////////////////////////////////////////////////////
+
+typedef struct referenceCoordinate_st ReferenceCoordinate;
+static Coordinate reference_coordinate_double_strand = true;
+
+struct referenceCoordinate_st {
+	char * name;
+	Coordinate start;
+	Coordinate finish;
+	IDnum referenceID;
+	IDnum counter;
+	boolean positive_strand;
+}  ATTRIBUTE_PACKED;
+
+static int compareRefCoords(const void * ptrA, const void * ptrB) {
+	ReferenceCoordinate * A = (ReferenceCoordinate *) ptrA;
+	ReferenceCoordinate * B = (ReferenceCoordinate *) ptrB;
+	int comp = strcmp(A->name, B->name);
+
+	if (comp != 0)
+		return comp;
+	else if (!reference_coordinate_double_strand && A->positive_strand != B->positive_strand)
+		return A->positive_strand > B->positive_strand;
+	else {
+		if (A->finish > -1 && A->finish < B->start)
+			return -1;
+		else if (B->finish > -1 && A->start > B->finish) 
+			return 1;
+		else return 0;
+	}
+}
+
+typedef struct referenceCoordinateTable_st ReferenceCoordinateTable;
+
+struct referenceCoordinateTable_st {
+	ReferenceCoordinate * array;
+	IDnum arrayLength;
+}  ATTRIBUTE_PACKED;
+
+static ReferenceCoordinateTable * newReferenceCoordinateTable() {
+	ReferenceCoordinateTable * table = callocOrExit(1, ReferenceCoordinateTable);
+	table->array = NULL;
+	table->arrayLength = 0;
+	return table;
+}
+
+static void printReferenceCoordinateTableStats(ReferenceCoordinateTable * table) {
+	IDnum index;
+	IDnum counter = 0;
+
+	velvetLog("Reference mapping counters\n");
+	velvetLog("Name\tRead mappings\n");
+
+	for (index = 0; index < table->arrayLength; index++) {
+		velvetLog("%s\t%li\n", table->array[index].name, (long) table->array[index].counter);
+		counter += table->array[index].counter;
+	}
+
+	if (counter == 0) {
+		velvetLog("WARNING: None of your read mappings recognized the reference sequence!\n");
+		velvetLog("Double check that the names are identical between reference fasta headers and SAM/BAM sequences.\n");
+	}
+}
+
+static void destroyReferenceCoordinateTable(ReferenceCoordinateTable * table) {
+	IDnum index;
+
+	if (table->array) {
+		printReferenceCoordinateTableStats(table);
+		for (index = 0; index < table->arrayLength; index++)
+			free(table->array[index].name);
+		free(table->array);
+	}
+	free(table);
+}
+
+static void resizeReferenceCoordinateTable(ReferenceCoordinateTable * table, IDnum extraLength) {
+	if (table->array == NULL)
+		table->array = callocOrExit(extraLength, ReferenceCoordinate);
+	else 
+		table->array = reallocOrExit(table->array, table->arrayLength + extraLength, ReferenceCoordinate);
+}
+
+static ReferenceCoordinate * findReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {
+	ReferenceCoordinate * array = table->array;
+	ReferenceCoordinate refCoord;
+	Coordinate leftIndex = 0;
+	Coordinate rightIndex = table->arrayLength - 1;
+	Coordinate middleIndex;
+
+	refCoord.name = name;
+	refCoord.start = start;
+	refCoord.finish = finish;
+	refCoord.referenceID = 0;
+	refCoord.positive_strand = positive_strand;
+
+	while (true) {
+		middleIndex = (rightIndex + leftIndex) / 2;
+
+		if (leftIndex > rightIndex)
+			return NULL;
+		else if (compareRefCoords(&(array[middleIndex]), &refCoord) == 0)
+			return &(array[middleIndex]);
+		else if (leftIndex == middleIndex)
+			return NULL;
+		else if (compareRefCoords(&(array[middleIndex]), &refCoord) > 0)
+			rightIndex = middleIndex;
+		else
+			leftIndex = middleIndex;
+	}
+}
+
+static void addReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {
+	ReferenceCoordinate * refCoord;
+
+	if ((refCoord = findReferenceCoordinate(table, name, start, finish, positive_strand))) {
+		velvetLog("Overlapping reference coordinates:\n");
+		velvetLog("%s:%lli-%lli\n", name, (long long) start, (long long) finish);
+		velvetLog("%s:%lli-%lli\n", refCoord->name, (long long) refCoord->start, (long long) refCoord->finish);
+		velvetLog("Exiting...\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+	
+	refCoord = &(table->array[table->arrayLength++]);
+
+	refCoord->name = name;
+	refCoord->start = start;
+	refCoord->finish = finish;
+	refCoord->referenceID = table->arrayLength;
+	refCoord->positive_strand = positive_strand;
+	refCoord->counter = 0;
+}
+
+static void sortReferenceCoordinateTable(ReferenceCoordinateTable * table) {
+	qsort(table->array, table->arrayLength, sizeof(ReferenceCoordinate), compareRefCoords);
+}
+
+//////////////////////////////////////////////////////////////////////////
+// File reading 
+//////////////////////////////////////////////////////////////////////////
+
+static void velvetifySequence(char * str, SequencesWriter *seqWriteInfo) {
+	int i;
+	char c;
+	size_t length = strlen(str);
+
+	for (i = 0; i < length; i++) {
+		c = str[i];
+		switch (c) {
+		case '\n':
+		case '\r':
+		case EOF:
+			str[i] = '\0';
+			break;
+		case 'A':
+		case 'a':
+			str[i] = 'A';
+			break;
+		case 'C':
+		case 'c':
+			str[i] = 'C';
+			break;
+		case 'G':
+		case 'g':
+			str[i] = 'G';
+			break;
+		case 'T':
+		case 't':
+			str[i] = 'T';
+			break;
+		default:
+			str[i] = 'N';
+		}
+		// non NULL indicates ref masks are being created
+		if (seqWriteInfo->m_referenceMask != NULL) {
+			if (str[i] == 'N') {
+				if (seqWriteInfo->m_openMask) {
+					seqWriteInfo->m_current->finish++;
+				} else if (*(seqWriteInfo->m_referenceMask) == NULL) {
+					*(seqWriteInfo->m_referenceMask) = newMask(seqWriteInfo, seqWriteInfo->m_position);
+					seqWriteInfo->m_current = *(seqWriteInfo->m_referenceMask);
+				} else {
+					seqWriteInfo->m_current->next = newMask(seqWriteInfo, seqWriteInfo->m_position);
+					seqWriteInfo->m_current = seqWriteInfo->m_current->next;		
+				}
+				seqWriteInfo->m_openMask = true;
+				seqWriteInfo->m_position += 1;
+			} else if (str[i] != '\0') {
+				seqWriteInfo->m_openMask = false;
+				seqWriteInfo->m_position += 1;
+			}
+		}
+	} 
+}
+
+static void reverseComplementSequence(char * str)
+{
+	size_t length = strlen(str);
+	size_t i;
+
+	for (i = 0; i < length-1 - i; i++) {
+		char c = str[i];
+		str[i] = str[length-1 - i];
+		str[length-1 - i] = c;
+	}
+
+#ifndef COLOR
+	for (i = 0; i < length; i++) {
+		switch (str[i]) {
+		case 'A':
+		case 'a':
+			str[i] = 'T';
+			break;
+		case 'C':
+		case 'c':
+			str[i] = 'G';
+			break;
+		case 'G':
+		case 'g':
+			str[i] = 'C';
+			break;
+		// As in velvetifySequence(), anything unusual ends up as 'A'
+		default:
+			str[i] = 'A';
+			break;
+		}
+	}
+#endif
+}
+
+static void writeFastaSequence(FILE * outfile, const char * str)
+{
+	size_t length = strlen(str);
+	size_t start;
+	for (start = 0; start < length; start += 60)
+		velvetFprintf(outfile, "%.60s\n", &str[start]);
+}
+
+void convertSequences(ReadSet * rs)
+{
+	rs->tSequences = newTightStringArrayFromStringArray(rs->sequences,
+							    rs->readCount,
+							    &rs->tSeqMem);
+	rs->sequences = NULL;
+}
+
+// Returns the value of a 32-bit little-endian-stored integer.
+static int int32(const unsigned char * ptr)
+{
+	int x = ptr[3];
+	x = (x << 8) | ptr[2];
+	x = (x << 8) | ptr[1];
+	x = (x << 8) | ptr[0];
+	return x;
+}
+
+void goToEndOfLine(char *line, FILE * file)
+{
+	size_t length = strlen(line);
+	char c = line[length - 1];
+
+	while (c != '\n')
+		c = fgetc(file);
+}
+
+static void writeSeqName(char*seq_name, SequencesWriter *seqWriteInfo, Category cat, IDnum *sequenceIndex)
+{
+	char name[5001];
+	if (isCreateBinary()) {
+	  	cnySeqInsertStart(seqWriteInfo);
+		sprintf(name, ">%s", seq_name);
+		cnySeqInsertSequenceName(name, (long) ((*sequenceIndex)++), seqWriteInfo, cat);
+	} else {
+		velvetFprintf(seqWriteInfo->m_pFile,">%s\t%ld\t%d\n", seq_name, (long) ((*sequenceIndex)++), (int) cat);
+	}
+}
+
+static void writeSequence(char*seq, SequencesWriter *seqWriteInfo)
+{
+	char str[100];
+	velvetifySequence(seq, seqWriteInfo);
+	if (isCreateBinary()) {
+		cnySeqInsertNucleotideString(seq, seqWriteInfo);
+		cnySeqInsertEnd(seqWriteInfo);
+	} else {
+		Coordinate start = 0;
+		while (start <= strlen(seq)) {
+			strncpy(str, seq + start, 60);
+			str[60] = '\0';
+				velvetFprintf(seqWriteInfo->m_pFile, "%s\n", str);
+			start += 60;
+		}
+	}
+}
+
+static void initFastX(SequencesWriter *seqWriteInfo, Category cat)
+{
+	seqWriteInfo->m_referenceMask = NULL;
+	seqWriteInfo->m_position = 0;
+	seqWriteInfo->m_openMask = false;
+
+	// Binary file stuff
+	if (isCreateBinary() && (cat == REFERENCE)) {
+		seqWriteInfo->m_referenceMask = callocOrExit(1, Mask*);
+	}
+	if (isCreateBinary()) {
+		inputCnySeqFileStart(cat, seqWriteInfo);
+	}
+}
+
+static void cleanupFastX(SequencesWriter *seqWriteInfo, Category cat)
+{
+	if (seqWriteInfo->m_referenceMask) {
+		free(seqWriteInfo->m_referenceMask);
+		seqWriteInfo->m_referenceMask = NULL;
+	}
+}
+
+
+// Imports sequences from a raw sequence file
+// Memory space allocated within this function.
+static void readRawFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex)
+{
+	FILE *file;
+	const int maxline = 5000;
+	char line[5000];
+	IDnum counter = 0;
+
+	initFastX(seqWriteInfo, cat);
+
+	if (strcmp(filename, "-"))
+		file = fopen(filename, "r");
+	else 
+		file = stdin;
+
+	if (file != NULL)
+		velvetLog("Reading raw file %s\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	while(fgets(line, maxline, file)) { 
+		if (strlen(line) >= maxline - 1) {
+			velvetLog("Raw sequence files cannot contain reads longer than %i bp\n", maxline - 1);
+#ifdef DEBUG
+			abort();
+#endif
+			exit(1);
+		}
+
+		writeSeqName("RAW", seqWriteInfo, cat, sequenceIndex);
+		writeSequence(line, seqWriteInfo);
+		counter++;
+	}
+	fclose(file);
+	cleanupFastX(seqWriteInfo, cat);
+	velvetLog("%li reads found.\n", (long) counter);
+	velvetLog("Done\n");
+}
+
+// Imports sequences from a zipped raw file 
+// Memory space allocated within this function.
+static void readRawGZFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex)
+{
+	gzFile file;
+	const int maxline = 5000;
+	char line[5000];
+	IDnum counter = 0;
+
+	initFastX(seqWriteInfo, cat);
+	if (strcmp(filename, "-"))
+		file = gzopen(filename, "rb");
+	else { 
+		file = gzdopen(fileno(stdin), "rb");
+		SET_BINARY_MODE(stdin);
+	}
+
+	if (file != NULL)
+		velvetLog("Reading zipped raw sequence file %s\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	while(gzgets(file, line, maxline)) {
+		if (strlen(line) >= maxline - 1) {
+			velvetLog("Raw sequence files cannot contain reads longer than %i bp\n", maxline - 1);
+#ifdef DEBUG
+			abort();
+#endif
+			exit(1);
+		}
+
+		writeSeqName("RAW", seqWriteInfo, cat, sequenceIndex);
+		writeSequence(line, seqWriteInfo);
+		counter++;
+	}
+	gzclose(file);
+	cleanupFastX(seqWriteInfo, cat);
+	velvetLog("%li reads found.\n", (long) counter);
+	velvetLog("Done\n");
+}
+
+static void fillReferenceCoordinateTable(char *filename, ReferenceCoordinateTable * refCoords, IDnum counter)
+{
+	FILE *file;
+	const int maxline = 5000;
+	char line[5000];
+	char * name;
+	long long start, finish;
+	Coordinate i;
+	IDnum index = 0;
+
+	if (strcmp(filename, "-") == 0)
+		exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence from stdin");
+	else
+		file = fopen(filename, "r");
+
+	if (counter == 0)
+		return;
+
+	resizeReferenceCoordinateTable(refCoords,counter);
+
+	while (fgets(line, maxline, file) && index < counter) {
+		if (line[0] == '>') {
+			name = callocOrExit(strlen(line), char);
+
+			if (strchr(line, ':')) {
+				sscanf(strtok(line, ":-\r\n\t "), ">%s", name);
+				sscanf(strtok(NULL, ":-\r\n\t "), "%lli", &start);
+				sscanf(strtok(NULL, ":-\r\n\t "), "%lli", &finish);
+				if (start <= finish)
+					addReferenceCoordinate(refCoords, name, start, finish, true);
+				else
+					addReferenceCoordinate(refCoords, name, finish, start, false);
+			} else {
+				// Chomping EOL characters and comments
+				for (i=strlen(line) - 1; i >= 0; i--)
+					if (line[i] == '\n' || line[i] == '\r' || line[i] == ' ' || line[i] == '\t')
+						line[i] = '\0';
+
+				strcpy(name, line + 1);
+				addReferenceCoordinate(refCoords, name, 1, -1, true);
+			}
+
+			index++;
+		}
+	}
+
+	sortReferenceCoordinateTable(refCoords);
+}
+
+#define FASTQ 1
+#define FASTA 2
+#define FASTA_GZ 5
+#define FASTQ_GZ 6
+#define SAM 8
+#define BAM 9
+#define RAW 10
+#define RAW_GZ 11
+#define AUTO 12
+
+static gzFile openFastXFile(int fileType, char*filename)
+{
+	gzFile file;
+	char c;
+
+    	// Choose file or stdin
+	if (strcmp(filename, "-")==0) {
+		file = gzdopen(fileno(stdin), "rb");
+		SET_BINARY_MODE(stdin);
+	} else {
+		file = gzopen(filename, "rb");
+	}
+
+	// Verify filetype
+	c = gzgetc(file);
+	switch (fileType) {
+	case FASTA:
+	case FASTA_GZ:
+	  if (c != EOF && c!='>')
+	    exitErrorf(EXIT_FAILURE, false, "%s does not seem to be in FastA format", filename);
+	  break;
+	case FASTQ:
+	case FASTQ_GZ:
+	  if (c != EOF && c!='@')
+	    exitErrorf(EXIT_FAILURE, false, "%s does not seem to be in FastQ format", filename);
+	  break;
+	}
+	gzungetc(c, file);
+
+
+	if (file != NULL) {
+		char *type;
+		switch (fileType) {
+		case FASTA:
+		case FASTA_GZ: type = "FastA"; break;
+		case FASTQ:
+		case FASTQ_GZ: type = "FastQ"; break;
+		default: type = ""; break;
+		}
+		velvetLog("Reading %s file %s;\n", type, filename);
+	} else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	return file;
+}
+
+typedef struct {
+	gzFile gzFile;
+	AutoFile *autoFile;
+} FileGZOrAuto;
+
+size_t fileGZOrAuto_read(FileGZOrAuto kseq_file, void *ptr, size_t size)
+{
+	if (kseq_file.gzFile)
+        	return gzread(kseq_file.gzFile, ptr, size);
+        else
+          return fread(ptr, 1, size, kseq_file.autoFile->file);
+}
+
+void fileGZOrAuto_close(FileGZOrAuto kseq_file)
+{
+	if (kseq_file.gzFile)
+        	gzclose(kseq_file.gzFile);
+        else
+          closeFileAuto(kseq_file.autoFile);
+}
+
+char const* charToType(char c)
+{
+	switch(c) {
+        case '>': return "FastA";
+        case '@': return "FastQ";
+        default: return "Unknown";
+        }
+}
+
+// Define mode to use kseq in
+KSEQ_INIT(FileGZOrAuto, fileGZOrAuto_read)
+
+// Read in FastA or FastQ files in compressed or gz format
+static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex, ReferenceCoordinateTable * refCoords)
+{
+	kseq_t *seq;
+	FileGZOrAuto file;
+	IDnum counter = 0;
+
+        file.gzFile = file.autoFile = NULL;
+        if (fileType == AUTO) {
+        	file.autoFile = openFileAuto(filename);
+                if (!file.autoFile)
+                	exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename);
+                velvetLog("Reading file '%s' using '%s' as %s\n", filename, file.autoFile->decompressor, charToType(file.autoFile->first_char));
+        } else
+          file.gzFile = openFastXFile(fileType, filename);
+
+	initFastX(seqWriteInfo, cat);
+	// Read a sequence at a time
+	seq = kseq_init(file);
+	while (kseq_read(seq) >= 0) {
+		counter++;
+		writeSeqName(seq->name.s, seqWriteInfo, cat, sequenceIndex);
+		writeSequence(seq->seq.s, seqWriteInfo);
+	}
+
+	kseq_destroy(seq);
+	fileGZOrAuto_close(file);
+
+  	if (cat == REFERENCE) {
+		fillReferenceCoordinateTable(filename, refCoords, counter);
+	}
+	cleanupFastX(seqWriteInfo, cat);
+
+	velvetLog("%li sequences found\n", (long) counter);
+	velvetLog("Done\n");
+}
+
+static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *filename1, char *filename2, Category cat, IDnum * sequenceIndex)
+{
+	kseq_t *seq1, *seq2;
+	FileGZOrAuto file1, file2;
+	IDnum counter = 0;
+
+	if (cat==REFERENCE)
+		exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode");
+
+        file1.gzFile = file1.autoFile = NULL;
+        file2.gzFile = file2.autoFile = NULL;
+        if (fileType == AUTO) {
+        	file1.autoFile = openFileAuto(filename1);
+                if (!file1.autoFile)
+                	exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename1);
+                velvetLog("Reading file '%s' using '%s' as %s\n", filename1, file1.autoFile->decompressor, charToType(file1.autoFile->first_char));
+        	file2.autoFile = openFileAuto(filename2);
+                if (!file2.autoFile)
+                	exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename2);
+                velvetLog("Reading file '%s' using '%s' as %s\n", filename2, file2.autoFile->decompressor, charToType(file2.autoFile->first_char));
+        } else {
+        	file1.gzFile = openFastXFile(fileType, filename1);
+                file2.gzFile = openFastXFile(fileType, filename2);
+        }
+	initFastX(seqWriteInfo, cat);
+
+	// Read a sequence at a time
+	seq1 = kseq_init(file1);
+	seq2 = kseq_init(file2);
+	while (kseq_read(seq1) >= 0) {
+		counter++;
+		writeSeqName(seq1->name.s, seqWriteInfo, cat, sequenceIndex);
+		writeSequence(seq1->seq.s, seqWriteInfo);
+
+		if (kseq_read(seq2) < 0)
+		  exitErrorf(EXIT_FAILURE, false, "Right sequence file '%s' has too few sequences", filename2);
+
+		counter++;
+		writeSeqName(seq2->name.s, seqWriteInfo, cat, sequenceIndex);
+		writeSequence(seq2->seq.s, seqWriteInfo);
+	}
+	if (kseq_read(seq2) >= 0)
+		  exitErrorf(EXIT_FAILURE, false, "Right sequence file '%s' has too many sequences", filename2);
+
+	kseq_destroy(seq1);
+	kseq_destroy(seq2);
+
+        fileGZOrAuto_close(file1);
+        fileGZOrAuto_close(file2);
+
+	cleanupFastX(seqWriteInfo, cat);
+
+	velvetLog("%li sequences found in total in the paired sequence files\n", (long) counter);
+	velvetLog("Done\n");
+}
+
+static void addMapping(boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
+	if (isCreateBinary()) {
+		seqWriteInfo->m_bIsRef = true;
+		RefInfoList *refElem = callocOrExit(1, RefInfoList);
+		if (refCoord->positive_strand) {
+			refElem->m_elem.m_referenceID = (long) orientation * refCoord->referenceID;
+			refElem->m_elem.m_pos = (long long) (pos - refCoord->start);
+		} else {
+			refElem->m_elem.m_referenceID = (long) -orientation * refCoord->referenceID;
+			refElem->m_elem.m_pos = (long long) (refCoord->finish - pos - strlen(seq));
+		}
+		refElem->next = NULL;
+		if (seqWriteInfo->m_refInfoHead == NULL) {
+			seqWriteInfo->m_refInfoHead = refElem;
+		} else {
+			(*refTail)->next = refElem;
+		}
+		*refTail = refElem;
+		seqWriteInfo->m_refCnt++;
+	} else {
+		if (refCoord->positive_strand) {
+			snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start));
+		} else 
+			snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq)));
+
+		if (*buffer_size - strlen(buffer) < 100) {
+			*buffer_size += 1000;
+			buffer = reallocOrExit(buffer, *buffer_size, char);
+		}
+	}
+
+	// Increment counter
+	refCoord->counter++;
+}
+
+static void writeMappedSequence(IDnum * sequenceIndex, Category cat, Category prev_cat, char * previous_seq, char * previous_qname, char * previous_qname_pairing, char * buffer, SequencesWriter * seqWriteInfo) {
+	char print_qname[5000];
+	if (isCreateBinary()) {
+		if (prev_cat != cat) {
+			inputCnySeqFileStart(cat, seqWriteInfo);
+			prev_cat = cat;
+		}
+		cnySeqInsertStart(seqWriteInfo);
+		cnySeqInsertNucleotideString(previous_seq, seqWriteInfo);
+		sprintf(print_qname, ">%s%s", previous_qname, previous_qname_pairing);
+		cnySeqInsertSequenceName(print_qname, (long) ((*sequenceIndex)++), seqWriteInfo, cat);
+		cnySeqInsertEnd(seqWriteInfo);
+	} else {
+		velvetFprintf(seqWriteInfo->m_pFile, ">%s%s\t%ld\t%d\n", previous_qname, previous_qname_pairing,
+		(long) ((*sequenceIndex)++), (int) cat);
+		writeFastaSequence(seqWriteInfo->m_pFile, previous_seq);
+		velvetFprintf(seqWriteInfo->m_pFile, "%s", buffer);
+		strcpy(buffer, "");
+	}
+}
+
+static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
+	long long cigar_num;
+	int cigar_index;
+	char c;
+
+	if (strlen(cigar) == 1 && cigar[0] == '*')
+		;
+	else {
+		cigar_num = 0;
+		for (cigar_index = 0; cigar_index < strlen(cigar); cigar_index++) {
+			c = cigar[cigar_index];
+			if (c == 'M' || c == '=' || c == 'X') {
+				if (refCoord->finish < 0 || pos < refCoord->finish)
+					addMapping(orientation, pos, seq, refCoord, buffer, seqWriteInfo, refTail, buffer_size);
+				cigar_num = 0;
+			} else if (c == 'S' || c == 'I') {
+				pos -= cigar_num;
+				cigar_num = 0;
+			} else if (c == 'D' || c == 'N') {
+				pos += cigar_num;
+				cigar_num = 0;
+			} else if (c == 'H' || c == 'P') {
+				cigar_num = 0;
+			} else if (isdigit(c)) {
+				cigar_num = 10 * cigar_num + (c - 48);
+			} else {
+				abort();
+			}
+		}
+	}
+}
+
+static void readSAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)
+{
+	char line[5000];
+	unsigned long lineno;
+	IDnum readCount = 0;
+	char previous_qname_pairing[10];
+	char previous_qname[5000];
+	char previous_seq[5000];
+	boolean previous_paired = false;
+	Category prev_cat = cat;
+	Category apparentCat;
+	ReferenceCoordinate * refCoord;
+	RefInfoList *refTail = NULL;
+	seqWriteInfo->m_referenceMask = NULL;   // no ref masks for SAM/BAM
+	seqWriteInfo->m_position = 0;
+	seqWriteInfo->m_openMask = false;
+
+	size_t buffer_size = 5000;
+	char * buffer = callocOrExit(buffer_size, char);
+
+	if (cat == REFERENCE) {
+		velvetLog("SAM file %s cannot contain reference sequences.\n", filename);
+		velvetLog("Please check the command line.\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+
+	FILE *file = (strcmp(filename, "-") != 0)? fopen(filename, "r") : stdin;
+	if (file)
+		velvetLog("Reading SAM file %s\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+	if (isCreateBinary()) {
+		inputCnySeqFileStart(cat, seqWriteInfo);
+	}
+	strcpy(previous_qname, "");
+	for (lineno = 1; fgets(line, sizeof(line), file); lineno++) {
+		if (line[0] != '@') {
+			char *qname, *flag, *seq, *rname, *cigar;
+			long long pos;
+			int orientation;
+			int i;
+
+			qname = strtok(line, "\t");
+			flag  = strtok(NULL, "\t");
+			rname = strtok(NULL, "\t");
+			sscanf(strtok(NULL, "\t"), "%lli", &pos);
+			orientation = 1;
+
+			// Mapping scor
+			(void) strtok(NULL, "\t");
+			cigar = strtok(NULL, "\t");
+
+			// Columns 7,8,9 are paired name, position and score
+			for (i = 7; i < 10; i++)
+				(void) strtok(NULL, "\t");
+			seq = strtok(NULL, "\t");
+
+			if (seq == NULL) {
+				velvetFprintf(stderr,
+					"Line #%lu: ignoring SAM record with too few fields\n",
+					lineno);
+			}
+			else if (strcmp(seq, "*") == 0) {
+				velvetFprintf(stderr,
+					"Line #%lu: ignoring SAM record with omitted SEQ field\n",
+					lineno);
+			}
+			else {
+				// Accept flags represented in either decimal or hex:
+				int flagbits = strtol(flag, NULL, 0);
+
+				if (flagbits & 0x4)
+				    strcpy(rname, "");
+
+				const char *qname_pairing = "";
+				if (flagbits & 0x40)
+					qname_pairing = "/1";
+				else if (flagbits & 0x80)
+					qname_pairing = "/2";
+
+				if (flagbits & 0x10) {
+					orientation = -1;
+					reverseComplementSequence(seq);
+				}
+
+				// Determine if paired to previous read
+				boolean same_name = (strcmp(qname, previous_qname) == 0);
+				if (readCount && (!same_name || strcmp(qname_pairing, previous_qname_pairing) != 0)) {
+					if (cat % 2 && !same_name && !previous_paired)
+						apparentCat = cat - 1;
+					else
+						apparentCat = cat;
+
+					previous_paired = (cat % 2 && same_name);
+
+					writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, buffer, seqWriteInfo);
+					prev_cat = apparentCat;
+				}
+
+				if (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, rname, (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation))) {
+					readCigar(cigar, orientation, pos, seq, refCoord, buffer, seqWriteInfo, &refTail, &buffer_size);
+				}
+
+				strcpy(previous_qname, qname);
+				strcpy(previous_qname_pairing, qname_pairing);
+				strcpy(previous_seq, seq);
+				velvetifySequence(previous_seq, seqWriteInfo);
+
+				readCount++;
+			}
+		}
+	}
+
+	if (readCount) {
+		if (cat % 2 && !previous_paired)
+			apparentCat = cat - 1;
+		else
+			apparentCat = cat;
+		writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, buffer, seqWriteInfo);
+	}
+
+	free(buffer);
+	fclose(file);
+	velvetLog("%lu reads found.\n", (long) readCount);
+	velvetLog("Done\n");
+}
+
+static int readBAMint32(gzFile file)
+{
+	unsigned char buffer[4];
+	if (gzread(file, buffer, 4) != 4)
+		exitErrorf(EXIT_FAILURE, false, "BAM file header truncated");
+
+	return int32(buffer);
+}
+
+static void readBAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)
+{
+	size_t seqCapacity = 0;
+	char *seq = NULL;
+	char cigar[5000];
+	char cigar_buffer[5000];
+	size_t bufferCapacity = 4;
+	unsigned char *buffer = mallocOrExit(bufferCapacity, unsigned char);
+	unsigned long recno, readCount;
+	int i, refCount;
+	gzFile file;
+	char previous_qname_pairing[10];
+	char previous_qname[5000];
+	char previous_seq[5000];
+	boolean previous_paired = false;
+	Category prev_cat = cat;
+	Category apparentCat;
+	char ** refNames;
+	ReferenceCoordinate * refCoord;
+	seqWriteInfo->m_referenceMask = NULL;   // no ref masks for SAM/BAM
+	seqWriteInfo->m_position = 0;
+	seqWriteInfo->m_openMask = false;
+
+	RefInfoList *refTail = NULL;
+	size_t mapBuffer_size = 1000;
+	char * mapBuffer = callocOrExit(mapBuffer_size, char);
+
+	if (cat == REFERENCE) {
+		velvetLog("BAM file %s cannot contain reference sequences.\n", filename);
+		velvetLog("Please check the command line.\n");
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+
+	if (strcmp(filename, "-") != 0)
+		file = gzopen(filename, "rb");
+	else {
+		file = gzdopen(fileno(stdin), "rb");
+		SET_BINARY_MODE(stdin);
+	}
+
+	if (file != NULL)
+		velvetLog("Reading BAM file %s\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	if (! (gzread(file, buffer, 4) == 4 && memcmp(buffer, "BAM\1", 4) == 0))
+		exitErrorf(EXIT_FAILURE, false, "%s is not in BAM format", filename);
+
+	// Skip header text
+	if (gzseek(file, readBAMint32(file), SEEK_CUR) == -1)
+		exitErrorf(EXIT_FAILURE, false, "gzseek failed");
+
+	// Skip header reference list
+	refCount = readBAMint32(file);
+	refNames = callocOrExit(refCount, char *);
+	for (i = 0; i < refCount; i++) {
+		int strLength;
+
+		if (gzread(file, buffer, 4) != 4)
+			exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
+
+		strLength = int32(buffer);
+		refNames[i] = callocOrExit(strLength, char);
+		
+		if (bufferCapacity < 4 + strLength) {
+			bufferCapacity = 4 + strLength + 4096;
+			buffer = reallocOrExit(buffer, bufferCapacity, unsigned char);
+		}
+
+		if (gzread(file, buffer, 4 + strLength) != 4 + strLength)
+			exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
+
+		strcpy(refNames[i], (char *) buffer); 
+	}
+	if (isCreateBinary()) {
+		inputCnySeqFileStart(cat, seqWriteInfo);
+	}
+	strcpy(previous_qname, "");
+	readCount = 0;
+	for (recno = 1; gzread(file, buffer, 4) == 4; recno++) {
+		int blockSize = int32(buffer);
+		int readLength;
+
+		if (bufferCapacity < 4 + blockSize) {
+			bufferCapacity = 4 + blockSize + 4096;
+			buffer = reallocOrExit(buffer, bufferCapacity, unsigned char);
+		}
+
+		if (gzread(file, &buffer[4], blockSize) != blockSize)
+			exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
+
+		readLength = int32(&buffer[20]);
+		if (readLength == 0) {
+			velvetFprintf(stderr,
+				"Record #%lu: ignoring BAM record with omitted SEQ field\n",
+				recno);
+		}
+		else {
+			int readNameLength = buffer[12];
+			int flag_nc = int32(&buffer[16]);
+			int flagbits = flag_nc >> 16;
+			int cigarLength = flag_nc & 0xffff;
+			char *qname = (char *)&buffer[36];
+			uint32_t *rawcigar = (uint32_t *) &buffer[36 + readNameLength];
+			unsigned char *rawseq =
+					&buffer[36 + readNameLength + 4 * cigarLength];
+			int rID = int32(&buffer[4]);
+			// NOTE: BAM file coords are 0-based, not 1-based like SAM files
+			// No comment
+			long long pos = int32(&buffer[8]) + 1;
+			int orientation = 1;
+
+			const char *qname_pairing = "";
+			if (flagbits & 0x40)
+				qname_pairing = "/1";
+			else if (flagbits & 0x80)
+				qname_pairing = "/2";
+
+			strcpy(cigar, "");
+			for (i = 0; i < cigarLength; i++) {
+				static const char decode_ops[] = "MIDNSHP=X";
+				uint32_t packed = *(rawcigar++);
+				sprintf(cigar_buffer, "%i%c", packed >> 4, decode_ops[packed & 0xf]);
+				strcat(cigar, cigar_buffer);
+			}
+
+			if (seqCapacity < readLength + 1) {
+				seqCapacity = readLength * 2 + 1;
+				seq = reallocOrExit(seq, seqCapacity, char);
+			}
+
+			for (i = 0; i < readLength; i += 2) {
+				static const char decode_bases[] = "=ACMGRSVTWYHKDBN";
+				unsigned int packed = *(rawseq++);
+				seq[i] = decode_bases[packed >> 4];
+				seq[i+1] = decode_bases[packed & 0xf];
+			}
+			seq[readLength] = '\0';
+
+			if (flagbits & 0x10) {
+				orientation = -1;
+				reverseComplementSequence(seq);
+			}
+
+			// Determine if paired to previous read
+			boolean same_name = (strcmp(qname, previous_qname) == 0);
+			if (readCount > 0 && (!same_name || strcmp(qname_pairing, previous_qname_pairing) != 0)) {
+				if (cat % 2 && !same_name && !previous_paired)
+					apparentCat = cat - 1;
+				else
+					apparentCat = cat;
+
+				previous_paired = (cat % 2 && same_name);
+
+				writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, mapBuffer, seqWriteInfo);
+				prev_cat = apparentCat;
+			}
+
+			if (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, refNames[rID], (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation)))
+				readCigar(cigar, orientation, pos, seq, refCoord, mapBuffer, seqWriteInfo, &refTail, &mapBuffer_size);
+
+			strcpy(previous_qname, qname);
+			strcpy(previous_qname_pairing, qname_pairing);
+			strcpy(previous_seq, seq);
+			velvetifySequence(previous_seq, seqWriteInfo);
+
+			readCount++;
+		}
+	}
+
+	if (readCount) {
+		if (cat % 2 && !previous_paired)
+			apparentCat = cat - 1;
+		else
+			apparentCat = cat;
+		writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, mapBuffer, seqWriteInfo);
+	}
+
+	free(seq);
+	free(buffer);
+	free(mapBuffer);
+
+	gzclose(file);
+	velvetLog("%lu reads found.\n", readCount);
+	velvetLog("Done\n");
+}
+
+
+static void printUsage()
+{
+	puts("Usage:");
+	puts("./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename} [options]");
+	puts("");
+	puts("\tdirectory\t\t: directory name for output files");
+	printf("\thash_length\t\t: odd integer (if even, it will be decremented) <= %i (if above, will be reduced)\n", MAXKMERLENGTH);
+	puts("\tfilename\t\t: path to sequence file or - for standard input");	
+	puts("");
+	puts("File format options:");
+	puts("\t-fasta");
+	puts("\t-fastq");
+	puts("\t-raw");
+	puts("\t-fasta.gz");
+	puts("\t-fastq.gz");
+	puts("\t-raw.gz");
+	puts("\t-sam");
+	puts("\t-bam");
+        puts("\t-fmtAuto");
+	puts("");
+	puts("Read type options:");
+	puts("\t-short");
+	puts("\t-shortPaired");
+	puts("\t-short2");
+	puts("\t-shortPaired2");
+	puts("\t-long");
+	puts("\t-longPaired");
+	puts("\t-reference");
+	puts("");
+	puts("Options:");
+	puts("\t-strand_specific\t: for strand specific transcriptome sequencing data (default: off)");
+	puts("");
+	puts("Output:");
+	puts("\tdirectory/Roadmaps");
+	puts("\tdirectory/Sequences");
+	puts("\t\t[Both files are picked up by graph, so please leave them there]");
+}
+
+// General argument parser for most functions
+// Basically a reused portion of toplevel code dumped into here
+void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand, boolean * noHash)
+{
+	int argIndex = 1;
+	int filetype = FASTA;
+	Category cat = 0;
+	IDnum sequenceIndex = 1;
+	short short_var;
+	ReferenceCoordinateTable * refCoords = newReferenceCoordinateTable();
+	boolean reuseSequences = false;
+	boolean separate_pair_files = false;
+
+	if (argc < 2) {
+		printUsage();
+#ifdef DEBUG 
+		abort();
+#endif 
+		exit(1);
+	}
+
+	for (argIndex = 1; argIndex < argc; argIndex++) {
+		if (strcmp(argv[argIndex], "-strand_specific") == 0) {
+			*double_strand = false;
+			reference_coordinate_double_strand = false;
+		} else if (strcmp(argv[argIndex], "-reuse_Sequences") == 0) {
+			reuseSequences = true;
+		} else if (strcmp(argv[argIndex], "-reuse_binary") == 0) {
+			reuseSequences = true;
+		} else if (strcmp(argv[argIndex], "-noHash") == 0) {
+			*noHash = true;
+		}
+	}
+
+	if (reuseSequences) 
+		return;
+
+	SequencesWriter * seqWriteInfo = NULL;
+	if (isCreateBinary()) {
+		seqWriteInfo = openCnySeqForWrite(filename);
+		seqWriteInfo->m_unifiedSeqFileHeader.m_bDoubleStrand = *double_strand;
+		// file is already open
+	} else {
+		seqWriteInfo = callocOrExit(1, SequencesWriter);
+		seqWriteInfo->m_pFile = fopen(filename, "w");
+	}
+
+	for (argIndex = 1; argIndex < argc; argIndex++) {
+		if (argv[argIndex][0] == '-' && strlen(argv[argIndex]) > 1) {
+
+			if (strcmp(argv[argIndex], "-fastq") == 0)
+				filetype = FASTQ;
+			else if (strcmp(argv[argIndex], "-fasta") == 0)
+				filetype = FASTA;
+			else if (strcmp(argv[argIndex], "-fastq.gz") == 0)
+				filetype = FASTQ_GZ;
+			else if (strcmp(argv[argIndex], "-fasta.gz") == 0)
+				filetype = FASTA_GZ;
+			else if (strcmp(argv[argIndex], "-sam") == 0)
+				filetype = SAM;
+			else if (strcmp(argv[argIndex], "-bam") == 0)
+				filetype = BAM;
+			else if (strcmp(argv[argIndex], "-raw") == 0)
+				filetype = RAW;
+			else if (strcmp(argv[argIndex], "-raw.gz") == 0)
+				filetype = RAW_GZ;
+			else if (strcmp(argv[argIndex], "-fmtAuto") == 0)
+				filetype = AUTO;
+			else if (strcmp(argv[argIndex], "-short") == 0)
+				cat = 0;
+			else if (strcmp(argv[argIndex], "-shortPaired") ==
+				 0)
+				cat = 1;
+			else if (strncmp
+				 (argv[argIndex], "-shortPaired",
+				  12) == 0) {
+				sscanf(argv[argIndex], "-shortPaired%hd", &short_var);
+				cat = (Category) short_var;
+				if (cat < 1 || cat > CATEGORIES) {
+					velvetLog("Unknown option: %s\n",
+					       argv[argIndex]);
+#ifdef DEBUG 
+					abort();
+#endif 
+					exit(1);
+				}
+				cat--;
+				cat *= 2;
+				cat++;
+			} else if (strncmp(argv[argIndex], "-short", 6) ==
+				   0) {
+				sscanf(argv[argIndex], "-short%hd", &short_var);
+				cat = (Category) short_var;
+				if (cat < 1 || cat > CATEGORIES) {
+					velvetLog("Unknown option: %s\n",
+					       argv[argIndex]);
+#ifdef DEBUG 
+					abort();
+#endif 
+					exit(1);
+				}
+				cat--;
+				cat *= 2;
+			} else if (strcmp(argv[argIndex], "-long") == 0)
+				cat = LONG;		// CATEGORIES * 2;
+			else if (strcmp(argv[argIndex], "-longPaired") == 0)
+				cat = LONG_PAIRED;	// CATEGORIES * 2 + 1;
+			else if (strcmp(argv[argIndex], "-reference") == 0)
+				cat = REFERENCE;	// CATEGORIES * 2 + 2
+			else if (strcmp(argv[argIndex], "-strand_specific") == 0) {
+				*double_strand = false;
+				reference_coordinate_double_strand = false;
+			} else if (strcmp(argv[argIndex], "-noHash") == 0) {
+				;
+			} else if (strcmp(argv[argIndex], "-create_binary") == 0) {
+				;
+			} else if (strcmp(argv[argIndex], "-interleaved") == 0) {
+				separate_pair_files = false;
+			} else if (strcmp(argv[argIndex], "-separate") == 0) {
+				separate_pair_files = true;
+			}
+			else {
+				velvetLog("Unknown option: %s\n",
+				       argv[argIndex]);
+#ifdef DEBUG 
+				abort();
+#endif 
+				exit(1);
+			}
+
+			continue;
+		}
+
+		if (cat == -1)
+			continue;
+
+		switch (filetype) {
+		case FASTA:
+		case FASTQ:
+		case FASTA_GZ:
+		case FASTQ_GZ:
+		case AUTO:
+			// Separate files for paired reads?  Note odd categories used for paired read type
+			if (separate_pair_files && cat%2==1) {
+				argIndex++;
+				if (argIndex>=argc)
+					exitErrorf(EXIT_FAILURE, false, "Require left & right filename for -separate mode");
+				readFastXPair(filetype, seqWriteInfo, argv[argIndex-1], argv[argIndex], cat, &sequenceIndex);
+			} else {
+				readFastXFile(filetype, seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
+			}
+			break;
+		case RAW:
+			if (separate_pair_files && cat%2==1) {
+                        	exitErrorf(EXIT_FAILURE, false, "Currently do not support -separate mode for RAW");
+                        }
+			readRawFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex);
+			break;
+		case RAW_GZ:
+			if (separate_pair_files && cat%2==1) {
+                        	exitErrorf(EXIT_FAILURE, false, "Currently do not support -separate mode for RAW");
+                        }
+			readRawGZFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex);
+			break;
+		case SAM:
+			readSAMFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
+			break;
+		case BAM:
+			readBAMFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
+			break;
+		default:
+			velvetLog("Screw up in parser... exiting\n");
+#ifdef DEBUG 
+			abort();
+#endif 
+			exit(1);
+		}
+	}
+
+	destroyReferenceCoordinateTable(refCoords);
+	if (isCreateBinary()) {
+		closeCnySeqForWrite(seqWriteInfo);
+	} else {
+		fclose(seqWriteInfo->m_pFile);
+}
+	if (seqWriteInfo) {
+	    free(seqWriteInfo);
+	}
+}
+
+void createReadPairingArray(ReadSet* reads)
+{
+	IDnum index;
+	IDnum *mateReads = mallocOrExit(reads->readCount, IDnum);
+	Category cat = 0;
+	int phase = 0;
+
+	for (index = 0; index < reads->readCount; index++) 
+		mateReads[index] = -1;
+
+	reads->mateReads = mateReads;
+
+	for (index = 0; index < reads->readCount; index++)
+	{
+		// Paired category
+		if (cat & 1)
+		{
+			// Leaving the paired category
+			if (reads->categories[index] != cat)
+			{
+				if (phase == 1)
+				{
+					reads->mateReads[index - 1] = -1;
+					reads->categories[index - 1]--;
+					phase = 0;
+				}
+				cat = reads->categories[index];
+				// Into another paired category
+				if (cat & 1)
+				{
+					reads->mateReads[index] = index + 1;
+					phase = 1;
+				}
+			}
+			else if (phase == 0)
+			{
+				reads->mateReads[index] = index + 1;
+				phase = 1;
+			}
+			else
+			{
+				reads->mateReads[index] = index - 1;
+				phase = 0;
+			}
+		}
+		// Leaving an unpaired category
+		else if (reads->categories[index] != cat)
+		{
+			cat = reads->categories[index];
+			// Into a paired category
+			if (cat & 1)
+			{
+				reads->mateReads[index] = index + 1;
+				phase = 1;
+			}
+		}
+	}
+}
+
+int pairedCategories(ReadSet * reads)
+{
+	boolean pairedCat[CATEGORIES + 1];
+	int pairedCatCount = 0;
+	IDnum index;
+
+	for (index = 0; index <= CATEGORIES; index++)
+		pairedCat[index] = 0;
+
+	for (index = 0; index < reads->readCount; index++) {
+		if (reads->categories[index] & 1 && !pairedCat[reads->categories[index] / 2]) {
+			pairedCat[reads->categories[index] / 2] = true;
+			if (pairedCatCount++ == CATEGORIES)
+				break;
+		} 	
+	}
+
+	return pairedCatCount;
+}
+
+boolean isSecondInPair(ReadSet * reads, IDnum index)
+{
+	return reads->secondInPair[index / 8] & (1 << (index & 7));
+}
+
+void computeSecondInPair(ReadSet * reads)
+{
+	IDnum index;
+	Category currentCat = 0;
+	Category previousCat = 0;
+	int phase = 0;
+
+	if (reads->secondInPair)
+		free (reads->secondInPair);
+	reads->secondInPair = callocOrExit((reads->readCount + 7) / 8, unsigned char);
+
+	for (index = 0; index < reads->readCount; index++)
+	{
+		currentCat = reads->categories[index];
+		if (currentCat & 1)
+		{
+			if (previousCat == currentCat)
+			{
+				if (phase == 0)
+				{
+					phase = 1;
+				}
+				else
+				{
+					reads->secondInPair[index / 8] |= (1 << (index & 7));
+					phase = 0;
+				}
+			}
+			else {
+				phase = 1;
+				if (index > 0 && previousCat & 1 && !isSecondInPair(reads, index - 1))
+				    reads->categories[index - 1] = (reads->categories[index - 1] / 2) * 2;
+			}
+		}
+		previousCat = currentCat;
+	}
+
+	// Safeguard against odd sets of reads
+	if (!isSecondInPair(reads, reads->readCount - 1)) {
+		reads->categories[reads->readCount - 1] = (reads->categories[reads->readCount - 1] / 2) * 2;
+	}
+}
+
+void detachDubiousReads(ReadSet * reads, boolean * dubiousReads)
+{
+	IDnum index;
+	IDnum pairID;
+	IDnum sequenceCount = reads->readCount;
+	IDnum *mateReads = reads->mateReads;
+
+	if (dubiousReads == NULL || mateReads == NULL)
+		return;
+
+	for (index = 0; index < sequenceCount; index++) {
+		if (!dubiousReads[index] || reads->categories[index] % 2 == 0 )
+			continue;
+
+		if (isSecondInPair(reads, index))
+		    pairID = index - 1;
+		else
+		    pairID = index + 1;
+
+		reads->categories[index] = (reads->categories[index] / 2) * 2;
+		reads->categories[pairID] = (reads->categories[pairID] / 2) * 2;
+	}
+}
+
+ReadSet *importReadSet(char *filename)
+{
+	FILE *file = fopen(filename, "r");
+	char *sequence = NULL;
+	Coordinate bpCount = 0;
+	const int maxline = 5000;
+	char line[5000];
+	IDnum sequenceCount, sequenceIndex;
+	ReadSet *reads;
+	short int temp_short;
+	int lineLength;
+
+	if (file != NULL)
+		velvetLog("Reading read set file %s;\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+	reads = newReadSet();
+
+	// Count number of separate sequences
+	sequenceCount = 0;
+	while (fgets(line, maxline, file) != NULL)
+		if (line[0] == '>')
+			sequenceCount++;
+	fclose(file);
+	velvetLog("%li sequences found\n", (long) sequenceCount);
+
+	reads->readCount = sequenceCount;
+	
+	if (reads->readCount == 0) {
+		reads->sequences = NULL;
+		reads->categories = NULL;
+		return reads;	
+	}
+
+	reads->sequences = callocOrExit(sequenceCount, char *);
+	reads->categories = callocOrExit(sequenceCount, Category);
+	// Counting base pair length of each sequence:
+	file = fopen(filename, "r");
+	sequenceIndex = -1;
+	while (fgets(line, maxline, file) != NULL) {
+		if (line[0] == '>') {
+
+			// Reading category info
+			sscanf(line, "%*[^\t]\t%*[^\t]\t%hd",
+			       &temp_short);
+			reads->categories[sequenceIndex + 1] = (Category) temp_short;
+
+			if (sequenceIndex != -1)
+				reads->sequences[sequenceIndex] =
+				    mallocOrExit(bpCount + 1, char);
+			sequenceIndex++;
+			bpCount = 0;
+		} if (line[0] == 'M') {;
+			// Map line
+		} else {
+			bpCount += (Coordinate) strlen(line) - 1;
+
+			if (sizeof(ShortLength) == sizeof(int16_t) && (bpCount > SHRT_MAX || bpCount < 0)) {
+				velvetLog("Read %li of length %lli, longer than limit %i\n",
+				       (long) sequenceIndex + 1, (long long) bpCount, SHRT_MAX);
+				velvetLog("You should modify recompile with the LONGSEQUENCES option (cf. manual)\n");
+				exit(1);
+			}
+		}
+	}
+
+	//velvetLog("Sequence %d has length %d\n", sequenceIndex, bpCount);
+	reads->sequences[sequenceIndex] =
+	    mallocOrExit(bpCount + 1, char);
+	fclose(file);
+
+	// Reopen file and memorize line:
+	file = fopen(filename, "r");
+	sequenceIndex = -1;
+	while (fgets(line, maxline, file)) {
+		if (line[0] == '>') {
+			if (sequenceIndex != -1) {
+				sequence[bpCount] = '\0';
+			}
+			sequenceIndex++;
+			bpCount = 0;
+			//velvetLog("Starting to read sequence %d\n",
+			//       sequenceIndex);
+			sequence = reads->sequences[sequenceIndex];
+		} else if (line[0] == 'M') {;
+			// Map line
+		} else {
+			lineLength = strlen(line) - 1;
+			strncpy(sequence + bpCount, line, lineLength);
+			bpCount += (Coordinate) lineLength;
+		}
+	}
+
+	sequence[bpCount] = '\0';
+	fclose(file);
+	computeSecondInPair(reads);
+
+	velvetLog("Done\n");
+	return reads;
+
+}
+
+void logInstructions(int argc, char **argv, char *directory)
+{
+	int index;
+	char *logFilename =
+	    mallocOrExit(strlen(directory) + 100, char);
+	FILE *logFile;
+	time_t date;
+	char *string;
+
+	time(&date);
+	string = ctime(&date);
+
+	strcpy(logFilename, directory);
+	strcat(logFilename, "/Log");
+	logFile = fopen(logFilename, "a");
+
+	if (logFile == NULL)
+		exitErrorf(EXIT_FAILURE, true, "Could not write to %s", logFilename);
+
+	velvetFprintf(logFile, "%s", string);
+
+	for (index = 0; index < argc; index++)
+		velvetFprintf(logFile, " %s", argv[index]);
+
+	velvetFprintf(logFile, "\n");
+
+	velvetFprintf(logFile, "Version %i.%i.%2.2i%s\n", VERSION_NUMBER,
+		RELEASE_NUMBER, UPDATE_NUMBER, VERSION_BRANCH);
+	velvetFprintf(logFile, "Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)\n");
+	velvetFprintf(logFile, "This is free software; see the source for copying conditions.  There is NO\n");
+	velvetFprintf(logFile, "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n");
+	velvetFprintf(logFile, "Compilation settings:\n");
+	velvetFprintf(logFile, "CATEGORIES = %i\n", CATEGORIES);
+	velvetFprintf(logFile, "MAXKMERLENGTH = %i\n", MAXKMERLENGTH);
+#ifdef _OPENMP
+	velvetFprintf(logFile, "OPENMP\n");
+#endif
+#ifdef LONGSEQUENCES
+	velvetFprintf(logFile, "LONGSEQUENCES\n");
+#endif
+#ifdef BIGASSEMBLY
+	velvetFprintf(logFile, "BIGASSEMBLY\n");
+#endif
+#ifdef COLOR
+	velvetFprintf(logFile, "COLOR\n");
+#endif
+#ifdef DEBUG
+	velvetFprintf(logFile, "DEBUG\n");
+#endif
+	velvetFprintf(logFile, "\n");
+
+	fclose(logFile);
+	free(logFilename);
+}
+
+void destroyReadSet(ReadSet * reads)
+{
+	IDnum index;
+
+	if (reads == NULL)
+		return;
+
+	if (reads->sequences != NULL)
+	{
+		for (index = 0; index < reads->readCount; index++)
+			free(reads->sequences[index]);
+		free(reads->sequences);
+	}
+
+	if (reads->tSequences != NULL)
+		free (reads->tSequences);
+
+	if (reads->tSeqMem != NULL)
+		free (reads->tSeqMem);
+
+	if (reads->labels != NULL)
+		for (index = 0; index < reads->readCount; index++)
+			free(reads->labels[index]);
+
+	if (reads->confidenceScores != NULL)
+		for (index = 0; index < reads->readCount; index++)
+			free(reads->confidenceScores[index]);
+
+	if (reads->kmerProbabilities != NULL)
+		for (index = 0; index < reads->readCount; index++)
+			free(reads->kmerProbabilities[index]);
+
+	free(reads->labels);
+	free(reads->confidenceScores);
+	free(reads->kmerProbabilities);
+	free(reads->mateReads);
+	free(reads->categories);
+	free(reads->secondInPair);
+	free(reads);
+}
+
+ShortLength *getSequenceLengths(ReadSet * reads, int wordLength)
+{
+	ShortLength *lengths = callocOrExit(reads->readCount, ShortLength);
+	IDnum index;
+	int lengthOffset = wordLength - 1;
+
+	for (index = 0; index < reads->readCount; index++)
+		lengths[index] =
+		    getLength(getTightStringInArray(reads->tSequences, index)) - lengthOffset;
+
+	return lengths;
+}