--- a/mrfast-2.1.0.4/CommandLineParser.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,388 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors: 
-        Farhad Hormozdiari
-        Faraz Hach
-	Can Alkan
-  Emails: 
-        farhadh AT uw DOT edu
-        fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu
-*/
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <getopt.h>
-#include <string.h>
-#include <ctype.h>
-#include "Common.h"
-#include "CommandLineParser.h"
-
-int						uniqueMode=1;
-int						indexingMode;
-int						searchingMode;
-int						pairedEndMode;
-int						pairedEndDiscordantMode;
-int						transChromosal=0;
-int						pairedEndProfilingMode;
-int						seqCompressed;
-int						outCompressed;
-int						cropSize = 0;
-int						progressRep = 0;
-int						minPairEndedDistance=-1;
-int						maxPairEndedDistance=-1;
-int						minPairEndedDiscordantDistance=-1;
-int						maxPairEndedDiscordantDistance=-1;
-int 					bestMode;
-int 					nosamMode;
-char					*seqFile1;
-char					*seqFile2;
-char					*mappingOutput = "output";
-char					*mappingOutputPath = "";
-char					*unmappedOutput = "unmapped";
-char					fileName[1000][2][FILE_NAME_LENGTH];
-int						fileCnt;
-int 					maxOEAOutput=1000;
-int 					maxDiscordantOutput=10000;
-unsigned char			errThreshold=2;
-unsigned char			maxHits=0;
-unsigned char			WINDOW_SIZE = 12;
-unsigned int			CONTIG_SIZE;
-unsigned int			CONTIG_MAX_SIZE;
-
-void printHelp();
-
-int parseCommandLine (int argc, char *argv[])
-{
-
-	int o;
-	int index;
-	char *fastaFile = NULL;
-	char *batchFile = NULL ;
-	int  batchMode = 0;
-		
-	static struct option longOptions[] = 
-	{
-		{"pe",				no_argument,		&pairedEndMode,		1},
-		{"discordant-vh",	        no_argument,		&pairedEndDiscordantMode,	1},
-		{"trans",                     no_argument,            &transChromosal        ,       1},
-		{"profile",			no_argument, 		&pairedEndProfilingMode,	1},
-		{"seqcomp",			no_argument,		&seqCompressed,		1},
-		{"outcomp",			no_argument,		&outCompressed,		1},
-		{"progress",		no_argument,		&progressRep,		1},
-		{"best",		no_argument,		&bestMode,		1},
-		{"index",			required_argument,	0, 					'i'},
-		{"search",			required_argument,	0,					's'},
-		{"help",			no_argument,		0,					'h'},
-		{"version",			no_argument,		0,					'v'},
-		{"seq",				required_argument,	0,					'x'},
-		{"seq1",			required_argument,	0,					'x'},
-		{"seq2",			required_argument,	0,					'y'},
-		{"ws",				required_argument,  0,					'w'},
-		{"min",				required_argument,  0,					'l'},
-		{"max",				required_argument,  0,					'm'},
-		{"crop",			required_argument,  0,					'c'},
-		{"maxoea",            required_argument,  0,                  'a'},
-		{"maxdis",            required_argument,  0,                  'd'},
-		{"nosam",        no_argument,        &nosamMode,      1},
-		{0,  0,  0, 0},
-	};
-
-	while ( (o = getopt_long ( argc, argv, "bhvn:e:o:u:i:s:x:y:w:l:m:c:a:d:", longOptions, &index)) != -1 )
-	{
-		switch (o)
-		{
-			case 'a':
-				maxOEAOutput = atoi(optarg);
-				break;
-			case 'd':
-				maxDiscordantOutput = atoi(optarg);
-				break;
-			case 'i':
-				indexingMode = 1;
-				fastaFile = optarg;
-				break;
-			case 's':
-				searchingMode = 1;
-				fastaFile = optarg;
-				break;
-			case 'b':
-				batchMode = 1;
-				break;
-			case 'c': 
-				cropSize = atoi(optarg);
-				break;
-			case 'w':
-				WINDOW_SIZE = atoi(optarg);
-				break;
-			case 'x':
-				seqFile1 = optarg;
-				break;
-			case 'y':
-				seqFile2 = optarg;
-				break;
-			case 'u':
-				unmappedOutput = optarg;
-				break;
-			case 'o':
-				mappingOutput = getMem(FILE_NAME_LENGTH);
-				mappingOutputPath = getMem(FILE_NAME_LENGTH);
-				stripPath (optarg, &mappingOutputPath, &mappingOutput);
-				break;
-			case 'n':
-				maxHits = atoi(optarg);
-				break;
-			case 'e':
-				errThreshold = atoi(optarg);
-				break;
-			case 'l':
-				minPairEndedDistance = atoi(optarg);
-				break;
-			case 'm':
-				maxPairEndedDistance = atoi(optarg);
-				break;					
-			case 'h':
-				printHelp();
-				return 0;
-				break;
-			case 'v':
-				fprintf(stdout, "%s.%s\n", versionNumber, versionNumberF);
-				return 0;
-				break;
-				/*		        case '?':
- 			        fprintf(stderr, "Unknown parameter: %s\n", longOptions[index].name);
-			        abort();
-				break;*/
-		}
-
-	}
-	if (indexingMode + searchingMode != 1)
-	{
-		fprintf(stdout, "ERROR: Indexing / Searching mode should be selected\n");
-		return 0;
-	}
-
-	if (WINDOW_SIZE > 15 || WINDOW_SIZE < 11)
-	{
-		fprintf(stdout, "ERROR: Window size should be in [12..15]\n");
-		return 0;
-	}
-
-
-	if ( indexingMode )
-	{
-		CONTIG_SIZE		= 15000000;
-		CONTIG_MAX_SIZE	= 40000000;
-
-		if (batchMode)
-		{
-			batchFile = fastaFile;
-			fastaFile = NULL;
-		}
-
-		if (batchFile == NULL && fastaFile == NULL)
-		{
-			fprintf(stdout, "ERROR: Reference(s) should be indicated for indexing\n");
-			return 0;
-		}
-
-		if (pairedEndDiscordantMode)
-		{
-			fprintf(stdout, "ERROR: --discordant cannot be used in indexing mode. \n");
-			return 0;
-		}
-
-	}
-
-
-	if ( searchingMode )
-	{
-		CONTIG_SIZE		= 300000000;
-		CONTIG_MAX_SIZE	= 300000000;
-
-
-		if (batchMode)
-		{
-			batchFile = fastaFile;
-			fastaFile = NULL;
-		}
-
-		if (batchFile == NULL && fastaFile == NULL)
-		{
-			fprintf(stdout, "ERROR: Index File(s) should be indiciated for searching\n");
-			return 0;
-		}
-
-		if (seqFile1 == NULL && seqFile2 == NULL)
-		{
-			fprintf(stdout, "ERROR: Please indicate a sequence file for searching.\n");
-			return 0;
-		}
-
-
-		if (!pairedEndMode && seqFile2 != NULL)
-		{
-			fprintf(stdout, "ERROR: Second File can be indicated in pairedend mode\n");
-			return 0;
-		}
-
-		if (pairedEndMode && (minPairEndedDistance <0 || maxPairEndedDistance < 0 || minPairEndedDistance > maxPairEndedDistance))
-		{
-			fprintf(stdout, "ERROR: Please enter a valid range for pairedend sequences.\n");
-			return 0;
-		}
-
-		if (pairedEndMode && seqFile1 == NULL)
-		{
-			fprintf(stdout, "ERROR: Please indicate the first file for pairedend search.\n");
-			return 0;
-		}
-
-		if (!pairedEndMode && pairedEndDiscordantMode)
-		{
-			fprintf(stdout, "ERROR: --discordant should be used with --pe");
-			return 0;
-		}
-
-		if (!pairedEndMode && pairedEndProfilingMode)
-		{
-			fprintf(stdout, "ERROR: --profile should be used with --pe");
-			return 0;
-		}
-	}
-
-	int i = 0;
-
-
-	if (batchMode)
-	{
-		FILE *fp = fileOpen(batchFile, "r");
-
-		if (fp == NULL)
-			return 0;
-
-		fileCnt  = 0;
-
-		while ( fgets(fileName[fileCnt][0], FILE_NAME_LENGTH, fp))
-		{
-			for (i = strlen(fileName[fileCnt][0])-1; i>=0; i--)
-				if ( !isspace(fileName[fileCnt][0][i]))
-					break;
-			fileName[fileCnt][0][i+1] = '\0';
-
-			if (strcmp(fileName[fileCnt][0], "") != 0)
-			{
-				sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]); 
-				fileCnt++;
-			}
-		}
-	}
-	else
-	{
-		sprintf(fileName[fileCnt][0], "%s", fastaFile);
-		sprintf(fileName[fileCnt][1], "%s.index", fileName[fileCnt][0]); 
-		fileCnt++;
-	}
-
-
-	if (pairedEndProfilingMode)
-	{
-
-		minPairEndedDistance = 0;
-		maxPairEndedDistance = 300000000;
-
-	}
-
-	if (pairedEndDiscordantMode)
-	{
-		minPairEndedDiscordantDistance = minPairEndedDistance;
-		maxPairEndedDiscordantDistance = maxPairEndedDistance;
-
-		minPairEndedDistance = 0;
-		maxPairEndedDistance = 300000000;
-	}
-
-	return 1;
-}
-
-
-void printHelp()
-{
-	char *errorType;
-	if (mrFAST)
-	{
-		fprintf(stdout,"mrFAST : Micro-Read Fast Alignment Search Tool.\n\n");
-		fprintf(stdout,"Usage: mrfast [options]\n\n");
-		errorType="edit distance";
-	}
-	else
-	{
-		fprintf(stdout,"mrsFAST : Micro-Read Substitutions (only) Fast Alignment Search Tool.\n\n");
-		fprintf(stdout,"mrsFAST is a cache oblivious read mapping tool. mrsFAST capable of mapping\n");
-		fprintf(stdout,"single and paired end reads to the reference genome. Bisulfite treated \n");
-		fprintf(stdout,"sequences are not supported in this version. By default mrsFAST reports  \n");
-		fprintf(stdout,"the output in SAM format.\n\n");
-		fprintf(stdout,"Usage: mrsFAST [options]\n\n");
-		errorType="hamming distance";
-	}
-
-	fprintf(stdout,"General Options:\n");
-	fprintf(stdout," -v|--version\t\tCurrent Version.\n");
-	fprintf(stdout," -h\t\t\tShows the help file.\n");
-	fprintf(stdout,"\n\n");
-
-	fprintf(stdout,"Indexing Options:\n");
-	fprintf(stdout," --index [file]\t\tGenerate an index from the specified fasta file. \n");
-	fprintf(stdout," -b\t\t\tIndicates the indexing will be done in batch mode.\n\t\t\tThe file specified in --index should contain the \n\t\t\tlist of fasta files.\n");
-	fprintf(stdout," --ws [int]\t\tSet window size for indexing (default:12 max:14).\n");
-	fprintf(stdout,"\n\n");
-
-	fprintf(stdout,"Searching Options:\n");
-	fprintf(stdout," --search [file]\tSearch in the specified genome. Provide the path to the fasta file. \n\t\t\tIndex file should be in the same directory.\n");
-	fprintf(stdout," -b\t\t\tIndicates the mapping will be done in batch mode. \n\t\t\tThe file specified in --search should contain the \n\t\t\tlist of fasta files.\n");
-	fprintf(stdout," --pe \t\t\tSearch will be done in Paired-End mode.\n");
-	fprintf(stdout," --seq [file]\t\tInput sequences in fasta/fastq format [file]. If \n\t\t\tpaired end reads are interleaved, use this option.\n");
-	fprintf(stdout," --seq1 [file]\t\tInput sequences in fasta/fastq format [file] (First \n\t\t\tfile). Use this option to indicate the first file of \n\t\t\tpaired end reads. \n");
-	fprintf(stdout," --seq2 [file]\t\tInput sequences in fasta/fastq format [file] (Second \n\t\t\tfile). Use this option to indicate the second file of \n\t\t\tpaired end reads.  \n");
-	fprintf(stdout," -o [file]\t\tOutput of the mapped sequences. The default is \"output\".\n");
-	fprintf(stdout," -u [file]\t\tSave unmapped sequences in fasta/fastq format.\n");
-        fprintf(stdout," --best   \t\tOnly the best mapping from all the possible mapping is returned.\n");
-	fprintf(stdout," --seqcomp \t\tIndicates that the input sequences are compressed (gz).\n");
-	fprintf(stdout," --outcomp \t\tIndicates that output file should be compressed (gz).\n");
-	fprintf(stdout," -e [int]\t\tMaximum allowed %s (default 2).\n", errorType);
-	fprintf(stdout," --min [int]\t\tMin distance allowed between a pair of end sequences.\n");
-	fprintf(stdout," --max [int]\t\tMax distance allowed between a pair of end sequences.\n");
-
-	fprintf(stdout," --maxoea [int]\t\tMax number of One End Anchored (OEA) returned for each read pair. We recommend 100 or above for NovelSeq use.\n");
-	fprintf(stdout," --maxdis [int]\t\tMax number of discordant map locations returned for each read pair. We recommend 300 or above for VariationHunter use.\n");
-}

--- a/mrfast-2.1.0.4/CommandLineParser.h	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors:
-        Farhad Hormozdiari
-        Faraz Hach
-        Can Alkan
-  Emails:
-        farhadh AT uw DOT edu
-        fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu                                                                                                                                                                                                              
-*/
-
-
-
-#ifndef __COMMAND_LINE_PARSER__
-#define __COMMAND_LINE_PARSER__
-
-int parseCommandLine (int argc, char *argv[]);
-
-#endif

--- a/mrfast-2.1.0.4/Common.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,184 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors: 
-	Farhad Hormozdiari
-        Faraz Hach
-	Can Alkan
-  Emails: 
-	farhadh AT uw DOT edu
-	fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu
- */
-
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/time.h>
-#include <zlib.h>
-#include <string.h>
-#include "Common.h"
-
-
-unsigned short 			SEQ_LENGTH = 0;
-long long				memUsage = 0;
-/**********************************************/
-FILE *fileOpen(char *fileName, char *mode)
-{
-	FILE *fp;
-	fp = fopen (fileName, mode);
-	if (fp == NULL)
-	{
-		fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
-		fflush(stdout);
-		exit(0);
-	}
-	return fp;
-}
-/**********************************************/
-gzFile fileOpenGZ(char *fileName, char *mode)
-{
-	gzFile gzfp;
-	gzfp = gzopen (fileName, mode);
-	if (gzfp == Z_NULL)
-	{
-		fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
-		fflush(stdout);
-		exit(0);
-	}
-	return gzfp;
-}
-/**********************************************/
-double getTime(void)
-{
-	struct timeval t;
-	gettimeofday(&t, NULL);
-	return t.tv_sec+t.tv_usec/1000000.0;
-}
-
-/**********************************************/
-char reverseCompleteChar(char c)
-{
-	char ret;
-	switch (c)
-	{
-		case 'A': 
-					ret = 'T';
-					break;
-		case 'T':
-					ret = 'A';
-					break;
-		case 'C':	
-					ret = 'G';
-					break;
-		case 'G':
-					ret = 'C';
-					break;
-		default:
-					ret = 'N';
-					break;
-	}
-	return ret;
-}
-/**********************************************/
-void reverseComplete (char *seq, char *rcSeq , int length)
-{
-	int i;
-	for (i=0; i<length; i++)
-	{
-		rcSeq[i]=reverseCompleteChar (seq[length-1-i]) ;
-	}
-}
-/**********************************************/
-void * getMem(size_t size)
-{
-        void *ret;
-	ret = malloc(size);
-	if (ret == NULL){
-	  fprintf(stderr, "Cannot allocate memory. Currently addressed memory = %0.2f MB, requested memory = %0.2f MB.\nCheck the available main memory, and if you have user limits (ulimit -v).\n", getMemUsage(), (double)size);
-	  exit(0);
-	}
-	memUsage+=size;
-	return ret;
-}
-/**********************************************/
-void freeMem(void *ptr, size_t size)
-{
-	memUsage-=size;
-	free(ptr);
-}
-/**********************************************/
-double getMemUsage()
-{
-	return memUsage/1048576.0;
-}
-/**********************************************/
-void reverse (char *seq, char *rcSeq , int length)
-{
-	int i;
-	int l = length;
-	if(l != strlen(seq))
-		l = strlen(seq);
-	for (i=0; i<l; i++)
-	{
-		rcSeq[i]=seq[l-1-i] ;
-	}
-	rcSeq[l] = '\0';
-}
-/**********************************************/
-void stripPath(char *full, char **path, char **fileName)
-{
-	int i;
-	int pos = -1;
-
-	for (i=strlen(full)-1; i>=0; i--)
-	{
-		if (full[i]=='/')
-		{
-			pos = i;
-			break;
-		}
-
-	}
-
-	if (pos != -1)
-	{
-		sprintf(*fileName, "%s%c", (full+pos+1), '\0');
-		full[pos+1]='\0';
-		sprintf(*path,"%s%c", full, '\0');
-	}
-	else
-	{
-		sprintf(*fileName, "%s%c", full, '\0');
-		sprintf(*path,"%c", '\0');
-	}
-}

--- a/mrfast-2.1.0.4/Common.h	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors: 
-	Farhad Hormozdiari
-        Faraz Hach
-	Can Alkan
-  Emails: 
-	farhadh AT uw DOT edu
-	fhach AT cs DOT sfu DOT ca
-	calkan AT uw DOT edu
- */
-
-
-
-#ifndef __COMMON__
-#define __COMMON__
-
-#include <zlib.h>
-
-#define SEQ_MAX_LENGTH		300			// Seq Max Length
-#define CONTIG_OVERLAP		200 		// No. of characters overlapped between contings
-#define CONTIG_NAME_SIZE	200			// Contig name max size
-#define FILE_NAME_LENGTH	400			// Filename Max Length
-#define DISCORDANT_CUT_OFF	800
-#define MAX_OPEN_FILE		600		
-#define MAX_TRANS_CHROMOSAL_OUTPUT 50
-#define MAX_OEA_OUT		500
-
-extern unsigned int		CONTIG_SIZE;
-extern unsigned int		CONTIG_MAX_SIZE;
-
-
-extern unsigned char	WINDOW_SIZE				;		// WINDOW SIZE for indexing/searching
-extern unsigned short	SEQ_LENGTH;						// Sequence(read) length
-
-extern char				*versionNumber;
-extern char				*versionNumberF;
-extern unsigned char	mrFAST;
-
-
-extern int				maxOEAOutput;
-extern int				maxDiscordantOutput;
-extern int				uniqueMode;
-extern int				indexingMode;
-extern int				searchingMode;
-extern int				pairedEndMode;
-extern int				pairedEndDiscordantMode;
-extern int 				transChromosal;
-extern int				pairedEndProfilingMode;
-extern int				bestMode;
-extern int				nosamMode;
-extern int				seqCompressed;
-extern int				outCompressed;
-extern int				cropSize;
-extern int				progressRep;
-extern char 			*seqFile1;
-extern char				*seqFile2;
-extern char				*seqUnmapped;
-extern char				*mappingOutput;
-extern char 			*mappingOutputPath;
-extern char				*unmappedOutput;
-extern unsigned char	seqFastq;
-extern unsigned char	errThreshold;
-extern unsigned char	maxHits;	
-extern int				minPairEndedDiscordantDistance;
-extern int				maxPairEndedDiscordantDistance;
-extern int				minPairEndedDistance;
-extern int				maxPairEndedDistance;
-extern char				fileName[1000][2][FILE_NAME_LENGTH];
-extern int				fileCnt;
-extern long long		memUsage;
-
-FILE	* fileOpen(char *fileName, char *mode);
-gzFile	fileOpenGZ(char *fileName, char *mode);
-double	getTime(void);
-void	reverseComplete (char *seq, char *rcSeq , int length);
-void	* getMem(size_t size);
-void	freeMem(void * ptr, size_t size);
-double	getMemUsage();
-void 	reverse (char *seq, char *rcSeq , int length);
-void 	stripPath(char *full, char **path, char **fileName);
-#endif

--- a/mrfast-2.1.0.4/HashTable.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,472 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors: 
-	Farhad Hormozdiari
-        Faraz Hach
-	Can Alkan
-  Emails: 
-	farhadh AT uw DOT edu
-	fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu
-*/
-
-
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include "Common.h"
-#include "RefGenome.h"
-#include "HashTable.h"
-/**********************************************/
-FILE		*_ih_fp					= NULL;
-IHashTable	*_ih_hashTable			= NULL;
-int 		_ih_maxHashTableSize	= 0;
-char		*_ih_refGen				= NULL;
-char		*_ih_refGenName			= NULL;
-long long	_ih_memUsage			= 0;
-int			_ih_refGenOff			= 0;
-/**********************************************/
-
-int hashVal(char *seq)
-{
-	int i=0;
-	int val=0, numericVal=0;
-
-	while(i<WINDOW_SIZE)
-	{
-		switch (seq[i])
-		{
-			case 'A':
-				numericVal = 0;
-				break;
-			case 'C':
-				numericVal = 1;
-				break;
-			case 'G' :
-				numericVal = 2;
-				break;
-			case 'T':
-				numericVal = 3;
-				break;
-			default:
-				return -1;
-				break;
-		}
-		val = (val << 2)|numericVal;
-		i++;
-	}
-	return val;
-}
-/**********************************************/
-void freeIHashTableContent(IHashTable *hashTable, unsigned int maxSize)
-{
-	int i=0;
-	for (i=0; i<maxSize; i++)
-	{
-		if (hashTable[i].locs != NULL)
-		{
-			freeMem(hashTable[i].locs, (hashTable[i].locs[0]+1)*(sizeof(unsigned int)));
-			hashTable[i].locs = NULL;
-		}
-	}
-}
-/**********************************************/
-void initSavingIHashTable(char *fileName)
-{
-	int tmp;
-	_ih_fp = fileOpen(fileName, "w");
-	unsigned char bIndex = 0;				// Bisulfite Index
-	
-	// First Two bytes are indicating the type of the index & window size
-	tmp = fwrite(&bIndex, sizeof(bIndex), 1, _ih_fp);
-	tmp = fwrite(&WINDOW_SIZE, sizeof(WINDOW_SIZE), 1, _ih_fp);
-	
-	if (tmp == 0)
-	  fprintf(stderr, "Write error while initializing hash table.\n");
-
-}
-/**********************************************/
-void finalizeSavingIHashTable()
-{
-	fclose(_ih_fp);
-}
-/**********************************************/
-void saveIHashTable(IHashTable *hashTable,  unsigned int size, unsigned int maxSize, char *refGen, char *refGenName, int refGenOffset)
-{
-	int tmp;
-	
-	// Every Chunk starts with a byte indicating whether it has extra info;
-	unsigned char extraInfo = 0;
-	tmp = fwrite (&extraInfo, sizeof(extraInfo), 1, _ih_fp);
-
-	short len = strlen(refGenName);
-	tmp = fwrite(&len, sizeof(len), 1, _ih_fp);
-	tmp = fwrite(refGenName, sizeof(char), len, _ih_fp);
-
-	tmp = fwrite(&refGenOffset, sizeof(refGenOffset), 1, _ih_fp);
-	
-	unsigned int refGenLength = strlen(refGen);
-	tmp = fwrite(&refGenLength, sizeof(refGenLength), 1, _ih_fp);
-	
-	tmp = fwrite(refGen, sizeof(char), refGenLength, _ih_fp);
-	tmp = fwrite(&size, sizeof(size), 1, _ih_fp);
-
-	int i=0,j=0;
-	unsigned char cnt=0;
-	for (i=0; i<maxSize; i++)
-	{
-		if (hashTable[i].locs != NULL)
-		{
-			tmp = fwrite(&i, sizeof(i), 1, _ih_fp);
-
-			if (hashTable[i].locs[0] < 250)
-			{
-				cnt = hashTable[i].locs[0];
-				tmp = fwrite(&cnt, sizeof(cnt), 1, _ih_fp);
-			}
-			else
-			{
-				cnt =0;
-				tmp = fwrite (&cnt, sizeof(cnt), 1, _ih_fp);
-				tmp = fwrite (&(hashTable[i].locs[0]), sizeof(hashTable[i].locs[0]), 1, _ih_fp);
-			}
-
-			for (j=1; j<=hashTable[i].locs[0]; j++)
-				tmp = fwrite(&(hashTable[i].locs[j]), sizeof(hashTable[i].locs[j]), 1, _ih_fp);
-		}
-	}
-
-	if (tmp == 0)
-	  fprintf(stderr, "Write error while saving hash table.\n");
-}
-/**********************************************/
-unsigned int addIHashTableLocation(IHashTable *hashTable, int hv, int location)
-{
-	unsigned int	sizeInc				= 0;
-
-	if (hashTable[hv].locs == NULL)
-	{
-		sizeInc = 1;
-		hashTable[hv].locs = getMem (sizeof(unsigned int)*2);
-		hashTable[hv].locs[0]=1;
-		hashTable[hv].locs[1]=location;
-	}
-	else
-	{
-		int size = hashTable[hv].locs[0];
-		int i;
-		unsigned int *tmp = getMem( (size + 2) * sizeof(unsigned int) );
-
-		for (i = 0; i <= size; i++)
-		{
-			tmp[i] = hashTable[hv].locs[i];
-		}
-		size++;
-		tmp[0] = size;
-		tmp[size] = location;
-		
-		freeMem(hashTable[hv].locs, (hashTable[hv].locs[0]*(sizeof(unsigned int))));
-		hashTable[hv].locs = tmp;
-	}
-	return sizeInc;
-}
-/**********************************************/
-void generateIHashTable(char *fileName, char *indexName)
-{
-	double          startTime           = getTime();
-	unsigned int	hashTableSize		= 0;
-	unsigned int 	hashTableMaxSize	= pow(4, WINDOW_SIZE);
-	IHashTable		*hashTable			= getMem(sizeof(IHashTable)*hashTableMaxSize);
-	char 			*refGenName;
-	char			*refGen;
-	int				refGenOff			= 0;
-	int i, hv, l, flag;
-
-
-	for ( i = 0; i < hashTableMaxSize; i++)
-	{
-		hashTable[i].locs = NULL;
-	}
-
-	//Loading Fasta File
-	if (!initLoadingRefGenome(fileName))
-		return;		
-	initSavingIHashTable(indexName);
-	
-	fprintf(stdout, "Generating Index from %s", fileName);
-	fflush(stdout);
-
-	char *prev = getMem (CONTIG_NAME_SIZE);
-	prev[0]='\0';
-
-	do
-	{
-		flag = 	 loadRefGenome (&refGen, &refGenName, &refGenOff);	
-
-		if ( strcmp(prev, refGenName) != 0)
-		{
-			fprintf(stdout, "\n - %s ", refGenName);
-			fflush(stdout);
-			sprintf(prev, "%s", refGenName);
-		}
-		else
-		{
-			fprintf(stdout, ".");
-			fflush(stdout);
-		}
-		
-		l = strlen(refGen) - WINDOW_SIZE;
-
-		for (i=0; i < l; i++)
-		{
-			hv = hashVal(refGen + i);
-			if (hv != -1)
-			{
-				hashTableSize += addIHashTableLocation (hashTable, hv, i+1);
-			}
-		}
-
-		saveIHashTable(hashTable, hashTableSize, hashTableMaxSize, refGen, refGenName, refGenOff);
-		freeIHashTableContent(hashTable, hashTableMaxSize);
-		hashTableSize = 0;
-	} while (flag);
-
-	freeMem(prev, CONTIG_NAME_SIZE);
-	freeMem(hashTable, sizeof(IHashTable)*hashTableMaxSize);
-
-	finalizeLoadingRefGenome();
-	finalizeSavingIHashTable();
-
-	fprintf(stdout, "\nDONE in %0.2fs!\n", (getTime()-startTime));
-}
-
-/**********************************************/
-void finalizeLoadingIHashTable()
-{
-	freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
-	freeMem(_ih_hashTable, sizeof(IHashTable)* _ih_maxHashTableSize);
-	freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
-	freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
-	fclose(_ih_fp);
-}
-
-/**********************************************/
-int  loadIHashTable(double *loadTime, int errThreshould)
-{
-	double startTime = getTime();
-	unsigned char extraInfo = 0;
-	short len;
-	unsigned int refGenLength;
-	unsigned int hashTableSize;
-	unsigned int tmpSize;
-	int tmp;
-	int i=0,j=0;
-
-	if ( fread(&extraInfo, sizeof(extraInfo), 1, _ih_fp) != sizeof(extraInfo) )
-		return 0;
-
-	freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
-	freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
-	freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
-
-	// Reading Chr Name
-	tmp = fread(&len, sizeof(len), 1, _ih_fp);
-	if (tmp == 0){
-	  fprintf(stderr, "Read error while loading hash table.\n");
-	  exit(0);
-	}
-
-	_ih_refGenName = getMem(sizeof(char)* (len+1));
-	tmp = fread(_ih_refGenName, sizeof(char), len, _ih_fp);
-	_ih_refGenName [len] ='\0';
-
-	tmp = fread(&_ih_refGenOff, sizeof (_ih_refGenOff), 1, _ih_fp);
-
-	// Reading Size and Content of Ref Genome
-	tmp = fread(&refGenLength, sizeof(refGenLength), 1, _ih_fp);
-	_ih_refGen = getMem(sizeof(char)*(refGenLength+1));
-	tmp = fread(_ih_refGen, sizeof(char), refGenLength, _ih_fp);
-	_ih_refGen[refGenLength]='\0';
-
-	//Reading Hashtable Size and Content
-	tmp = fread(&hashTableSize, sizeof(hashTableSize), 1, _ih_fp);
-	
-	unsigned int hv;
-	unsigned char cnt=0;
-	unsigned int  index = 1;
-	unsigned int  tmpValue = 0;
-	for (i=0; i<hashTableSize; i++)
-	{
-		index = 1;
-		tmp = fread(&hv, sizeof(hv), 1, _ih_fp);
-		tmp = fread(&cnt, sizeof(cnt), 1, _ih_fp);
-
-		if (cnt>0)
-		{
-			tmpSize = cnt;
-		}
-		else
-		{
-			tmp = fread(&tmpSize, sizeof(tmpSize), 1, _ih_fp);
-		}
-		
-		_ih_hashTable[hv].locs = getMem( sizeof(unsigned int)* (tmpSize+1) );
-		_ih_hashTable[hv].locs[0] = tmpSize;
-
-/*		for (j=1; j<=tmpSize; j++) 
-			tmp = fread(&(_ih_hashTable[hv].locs[j]), sizeof(_ih_hashTable[hv].locs[j]), 1, _ih_fp);
-*/	
-		
-		if(tmpSize != 0)
-		{
-			tmp = fread(&(_ih_hashTable[hv].locs[index]), sizeof(_ih_hashTable[hv].locs[index]), 1, _ih_fp);
-			index++;
-		}
-
-		for (j=2; j<=tmpSize; j++)	
-		{
-			tmp = fread(&tmpValue, sizeof(_ih_hashTable[hv].locs[index-1]), 1, _ih_fp);
-			if(abs(tmpValue-_ih_hashTable[hv].locs[index-1]) >  errThreshould)
-			{
-				_ih_hashTable[hv].locs[index] = tmpValue;
-				index++;
-			}
-		}
-               _ih_hashTable[hv].locs[0] = index-1;
-	}
-	*loadTime = getTime()-startTime;
-	return 1;
-}
-/**********************************************/
-unsigned int *getIHashTableCandidates(int hv)
-{
-	if ( hv != -1 )
-		return _ih_hashTable[hv].locs;
-	else 
-		return NULL;
-}
-/**********************************************/
-/**********************************************/
-/**********************************************/
-void configHashTable()
-{
-	if (WINDOW_SIZE <= 15)
-	{
-		generateHashTable = &generateIHashTable;
-		loadHashTable = &loadIHashTable;
-		finalizeLoadingHashTable = &finalizeLoadingIHashTable;
-		getCandidates = &getIHashTableCandidates;
-	}
-	else
-	{
-
-
-	}
-}
-/**********************************************/
-int initLoadingHashTable(char *fileName)
-{
-	int i;	
-	unsigned char bsIndex;
-	int tmp; 
-
-	_ih_fp = fileOpen(fileName, "r");	
-
-	if (_ih_fp == NULL)
-		return 0;
-
-	tmp = fread(&bsIndex, sizeof(bsIndex), 1, _ih_fp);
-
-	if (tmp == 0){
-	  fprintf(stderr, "Read error while inilializing hash table loading.\n");
-	  exit(0);
-	}
-
-	if (bsIndex)
-	{
-		fprintf(stdout, "Error: Wrong Type of Index indicated");
-		return 0;
-	}
-	
-	tmp = fread(&WINDOW_SIZE, sizeof(WINDOW_SIZE), 1, _ih_fp);
-
-	configHashTable();
-
-	if (_ih_maxHashTableSize != pow(4, WINDOW_SIZE))
-	{
-
-		if (_ih_hashTable != NULL)
-		{
-			freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
-			freeMem(_ih_hashTable, sizeof(IHashTable)* _ih_maxHashTableSize);
-			freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
-			freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
-		}
-
-		_ih_maxHashTableSize = pow(4, WINDOW_SIZE);
-
-		_ih_hashTable = getMem (sizeof(IHashTable) * _ih_maxHashTableSize);
-		for (i=0; i<_ih_maxHashTableSize; i++)
-			_ih_hashTable[i].locs = NULL;
-		_ih_refGen = getMem(1);
-		_ih_refGen[0]='\0';
-		_ih_refGenName = getMem(1);
-		_ih_refGenName[0] = '\0';
-	}
-
-	return 1;
-}
-/**********************************************/
-char *getRefGenome()
-{
-	return _ih_refGen;
-
-}
-/**********************************************/
-char *getRefGenomeName()
-{
-	return _ih_refGenName;
-
-}
-/**********************************************/
-int getRefGenomeOffset()
-{
-	return _ih_refGenOff;
-
-}
-/**********************************************/
-HashTable *getHashTable()
-{
-	return NULL;
-}

--- a/mrfast-2.1.0.4/HashTable.h	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-  Authors: 
-	Farhad Hormozdiari
-        Faraz Hach
-	Can Alkan
-  Emails: 
-	farhadh AT uw DOT edu
-	fhach AT cs DOT sfu DOT ca
-	calkan AT uw DOT edu
- */
-
-
-
-#ifndef __HASH_TABLE__
-#define __HASH_TABLE__
-
-typedef struct HashTable
-{
-	long long hv;
-	int *locs; 
-} HashTable;
-
-typedef struct 
-{
-	unsigned int *locs;
-} IHashTable;
-
-int				hashVal(char *seq);
-void			configHashTable();
-char			*getRefGenome();
-char			*getRefGenomeName();
-int				getRefGenomeOffset();
-int				initLoadingHashTable(char *fileName);
-HashTable		*getHashTable();
-
-void 			(*generateHashTable)(char *fileName, char *indexName);
-int				(*loadHashTable)(double *loadTime, int errThreshould);
-void			(*finalizeLoadingHashTable)();
-unsigned int	*(*getCandidates)(int hv);
-
-#endif

--- a/mrfast-2.1.0.4/Makefile	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-CC=gcc
-CFLAGS = -c -O3 -Wall
-LDFLAGS = -lz -lm 
-SOURCES = baseFAST.c CommandLineParser.c Common.c HashTable.c MrFAST.c Output.c Reads.c RefGenome.c 
-OBJECTS = $(SOURCES:.c=.o)
-EXECUTABLE = mrfast
-
-
-all: $(SOURCES) $(EXECUTABLE)
-	rm -rf *.o
-		
-$(EXECUTABLE): $(OBJECTS) 
-	$(CC) $(OBJECTS) -o $@ $(LDFLAGS) 
-
-.c.o:
-	$(CC) $(CFLAGS) $< -o $@ 
-clean:
-	rm -f *.o *~ #*

--- a/mrfast-2.1.0.4/MrFAST.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8148 +0,0 @@
-/*
- * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification,
- * are permitted provided that the following conditions are met:
- *
- * Redistributions of source code must retain the above copyright notice, this list
- * of conditions and the following disclaimer.
- * - Redistributions in binary form must reproduce the above copyright notice, this
- *   list of conditions and the following disclaimer in the documentation and/or other
- *   materials provided with the distribution.
- * - Neither the names of the University of Washington, Simon Fraser University, 
- *   nor the names of its contributors may be
- *   used to endorse or promote products derived from this software without specific
- *   prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
- * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
- * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-/*
-Authors: 
-	Farhad Hormozdiari
-	Faraz Hach
-	Can Alkan
-Emails: 
-	farhadh AT uw DOT edu
-	fhach AT cs DOT sfu DOT ca
-        calkan AT uw DOT edu
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <math.h>
-#include <dirent.h>
-#include <xmmintrin.h>
-#include <emmintrin.h>
-#include <mmintrin.h>
-
-
-#include "Common.h"
-#include "Reads.h"
-#include "HashTable.h"
-#include "Output.h"
-#include "MrFAST.h"
-#include "RefGenome.h"
-
-
-#define min(a,b) ((a)>(b)?(b):(a))
-#define min3(a,b,c) ((a)>(b)?(b>c?c:b):(a>c?c:a))
-#define CHARCODE(a) (a=='A' ? 0 : (a=='C' ? 1 : (a=='G' ? 2 : (a=='T' ? 3 : 4))))
-
-#define MAX_REF_SIZE	18
-
-										
-float calculateScore(int index, char *seq, char *qual, char *md);
-unsigned char		mrFAST = 1;
-char				*versionNumberF="0.4";
-
-long long			verificationCnt = 0;
-long long 			mappingCnt = 0;
-long long			mappedSeqCnt = 0;
-long long			completedSeqCnt = 0;
-char				*mappingOutput;
-/**********************************************/
-char				*_msf_refGen = NULL;
-int				_msf_refGenLength = 0;
-int				_msf_refGenOffset = 0;
-char				*_msf_refGenName = NULL;
-
-int				_msf_refGenBeg;
-int				_msf_refGenEnd;
-
-IHashTable			*_msf_hashTable = NULL;
-
-int				*_msf_samplingLocs;
-int				*_msf_samplingLocsEnds;
-int				_msf_samplingLocsSize;
-
-Read				*_msf_seqList;
-int				_msf_seqListSize;
-
-Pair 				*_msf_sort_seqList = NULL;
-int 				*_msf_map_sort_seqList;
-
-ReadIndexTable			*_msf_rIndex = NULL;
-int				_msf_rIndexSize;
-int				_msf_rIndexMax;
-
-SAM				_msf_output;
-
-OPT_FIELDS			*_msf_optionalFields;
-
-char				*_msf_op;
-
-int				*_msf_verifiedLocs = NULL;
-
-char				_msf_numbers[200][3];
-char				_msf_cigar[5];
-
-MappingInfo			*_msf_mappingInfo;
-
-int				*_msf_seqHits;
-int				_msf_openFiles = 0;
-int				_msf_maxLSize=0;
-int				_msf_maxRSize=0;
-
-BestFullMappingInfo			*bestHitMappingInfo;
-
-/*************************/
-int				_msf_maxFile=0;
-char				_msf_fileName[4000][200][2][FILE_NAME_LENGTH];
-int				_msf_fileCount[4000];
-
-char				*_msf_readHasConcordantMapping; //boolean if a read has concordant mapping :D
-
-int 				*_msf_oeaMapping;
-int 				*_msf_discordantMapping;
-
-FILE *bestConcordantFILE;
-FILE *bestDiscordantFILE;
-
-int counter = 0;
-
-int scoreF[200][200];
-int scoreB[200][200];
-
-int score[200][200];
-int direction1[200][200];
-int direction2[200][200];
-
-__m128i MASK;
-
-int 			lookUpTable[15625][15625];
-
-/**************************************************Methods***************************************************/
-int smallEditDistanceF(char *a, int lena, char *b, int lenb)
-{
-        int matrix[20][20];
-        int i = 0;
-        int j = 0;
-
-        for(i = 0; i <= lena; i++)
-        {
-                matrix[0][i] = i;
-        }
-
-        for(i = 0; i <= lenb; i++)
-        {
-                matrix[i][0] = i;
-        }
-
-
-        for(i = 1; i <= lenb; i++)
-        {
-                for(j = 1; j <= lena; j++)
-                {
-                        matrix[i][j] = min3(matrix[i-1][j-1]+ (a[j-1] != b[i-1]),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
-                }
-        }
-        return (matrix[lenb][lena]>errThreshold?-1:matrix[lenb][lena]);
-}
-
-int smallEditDistanceB(char *a, int lena, char *b, int lenb)
-{
-        int matrix[20][20];
-        int i = 0;
-        int j = 0;
-	
-        for(i = 0; i <= lena; i++)
-        {
-                matrix[0][i] = i;
-        }
-
-        for(i = 0; i <= lenb; i++)
-        {
-                matrix[i][0] = i;
-        }
-
-
-        for(i = 1; i <= lenb; i++)
-        {
-                for(j = 1; j <= lena; j++)
-                {
-                        matrix[i][j] = min3(matrix[i-1][j-1]+ (*(a-j+1) != *(b-i+1)),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
-                }
-        }
-
-        return (matrix[lenb][lena]>errThreshold?-1:matrix[lenb][lena]);
-}
-
-char fastEditDistance(int per1, int per2)
-{
-
-	int i = 0;
-	int j = 0;
-
-	char str1[7];
-	char str2[7];
-
-	int val1 = per1;
-	int val2 = per2;
-
-	int index = 0;
-	int mod = 0;
-
-	int matrix[7][7];
-
-	int min = 20;
-
-	while(index < 6)
-	{
-		mod = val1%5;
-		str1[5-index] = (mod==0 ? 'A':(mod==1?'C':mod==2?'G':(mod==3)?'T':'N'));
-		val1 = val1 /5;
-		index++;
-	}
-
-	str1[6] = '\0';
-
-	index = 0;
-	while(index < 6)
-	{
-		mod=val2%5;
-		str2[5-index] = (mod==0 ? 'A':(mod==1?'C':mod==2?'G':(mod==3)?'T':'N'));
-		val2 = val2 / 5;
-		index++;
-	}
-	str2[6] = '\0';
-
-	for(i = 0; i < 7; i++)
-	{
-		matrix[0][i] = i;
-		matrix[i][0] = i;
-	}
-
-	for(i = 1; i < 7; i++)
-	{
-		for(j = 1; j < 7; j++)
-		{
-			matrix[i][j] = min3(matrix[i-1][j-1]+ (str1[i-1] != str2[j-1]),matrix[i][j-1]+1 ,matrix[i-1][j]+1);
-		}
-	}
-
-	for(i = 0; i < 7; i++)
-	{
-		if(matrix[i][6] < min)
-			min = matrix[i][6];
-	}
-
-	for(i = 0; i < 7; i++)
-	{
-		if(matrix[6][i] < min)
-			min = matrix[6][i];
-	}
-	return min;
-}
-
-void initLookUpTable()
-{
-	int i = 0; 
-
-	MASK = _mm_insert_epi16(MASK,1,0);
-	MASK = _mm_insert_epi16(MASK,1,1);
-	MASK = _mm_insert_epi16(MASK,1,2);
-	MASK = _mm_insert_epi16(MASK,1,3);
-	MASK = _mm_insert_epi16(MASK,1,4);
-	MASK = _mm_insert_epi16(MASK,0,5);
-	MASK = _mm_insert_epi16(MASK,0,6);
-	MASK = _mm_insert_epi16(MASK,0,7);
-
-	for(i = 0 ; i < errThreshold + 1; i++)
-	{
-		scoreF[0][i] = i;
-		scoreF[i][0] = i;
-	}
-
-	for(i = 0 ; i < errThreshold + 1; i++)
-	{
-		scoreB[0][i] = i;
-		scoreB[i][0] = i;
-	}
-
-
-}
-
-int backwardEditDistanceSSE2Odd(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-
-	int e = errThreshold;
-
-	char flag = 0;
-
-	int minError = 2*e;
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i Error;
-	__m128i tmp;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Error = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	if(lenb <= e) 
-	{
-		return smallEditDistanceB(a,lena,b,lenb);
-	}
-
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Side1 = _mm_xor_si128(Side1, Side1);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,2*e,1);
-
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,1,1);
-	Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-	R1 = _mm_insert_epi16(R1,1,0);
-	R1 = _mm_insert_epi16(R1,1,1);
-
-	for(i=2; i <= e; i++)
-	{
-		//set side
-		Side1 = _mm_slli_si128(Side1,2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_slli_si128(Down1,2);
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-
-			for(j=1;j<=i-1;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(i/2-1+(i/2-j))) != *(a-(i/2-1-(i/2-j))),0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R0 = _mm_min_epi16(R1+Side1, _mm_slli_si128(R0,2)+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down1);
-		}
-
-		else
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-			for(j=i/2-1;j>=-i/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i-1)/2-j-1)),0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down1);
-		}
-	}
-	Error = _mm_xor_si128(Error, Error);
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Error = _mm_insert_epi16(Error,e,0);
-	Side1 = _mm_insert_epi16(Side2,2*e,0);
-	Side2 = _mm_insert_epi16(Side2,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Side1 = _mm_slli_si128(Side1, 2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Error = _mm_slli_si128(Error, 2);
-		Error = _mm_insert_epi16(Error, e, 0);
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	for(; i <= 2*lenb-(e-1);i++)
-	{
-		flag = 0;
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			for(j=e/2;j>=-e/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(i/2-1+j)) != *(a-(i/2-1-j)),0);
-			}
-
-			R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-			R0 = _mm_min_epi16(R0, R1+Down1);
-
-
-			if(_mm_extract_epi16(R0,0) <= e)
-				flag = 1;
-			tmp = _mm_srli_si128(R0,2);
-			for(j=0; j <= e;j++)
-			{
-				if(_mm_extract_epi16(tmp,0) <= e)
-					flag = 1;
-				tmp = _mm_srli_si128(tmp,2);
-			}
-
-			if(flag == 0)
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			for(j=e/2;j>=-e/2-1;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i)/2-j-1)),0);
-			}
-
-			//	printf("@%d %d %d %d\n", _mm_extract_epi16(Diag,0), _mm_extract_epi16(Diag,1), _mm_extract_epi16(Diag,2),
-			//              _mm_extract_epi16(Diag,3));
-
-			R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-
-			//	printf("#~%d %d %d %d\n", _mm_extract_epi16(R1,0), _mm_extract_epi16(R1,1), _mm_extract_epi16(R1,2),
-			//              _mm_extract_epi16(R1,3));
-
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-			//	printf("$%d %d %d %d\n", _mm_extract_epi16(Side2,0), _mm_extract_epi16(Side2,1), _mm_extract_epi16(Side2,2),
-			//              _mm_extract_epi16(Side2,3));
-
-			//	printf("#%d %d %d %d\n", _mm_extract_epi16(R1,0), _mm_extract_epi16(R1,1), _mm_extract_epi16(R1,2),
-			//		_mm_extract_epi16(R1,3));    
-
-
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-	}
-
-	//first cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-3)) != *(a-lena), 0);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena-1)), 1);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena-2)), 2);
-	Diag = _mm_insert_epi16(Diag, 2*e, 3);
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-	
-	minError = min(minError, _mm_extract_epi16(R1,2));
-
-	//second cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena)), 0);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena-1)), 1);
-	Diag = _mm_insert_epi16(Diag, 2*e, 2);
-
-	R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0, R1+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R0,1));
-	
-	//third cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-2)) != *(a-(lena+1)), 0);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena)), 1);
-	Diag = _mm_insert_epi16(Diag, 2*e, 2);
-
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	//forth
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena+1)), 0);
-	Diag = _mm_insert_epi16(Diag, 2*e, 1);
-
-	R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0, R1+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	//fifth
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, *(b-(lenb-1)) != *(a-(lena+2)), 0);
-	Diag = _mm_insert_epi16(Diag, 2*e, 1);
-
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	if(minError > e)
-		return -1;
-	return minError;
-}
-
-int backwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-
-	int e = errThreshold;
-
-	char flag = 0;
-
-	int minError = 2*e;
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i Error;
-	__m128i tmp;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Error = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	if(lenb <= e) 
-	{
-		return smallEditDistanceB(a,lena,b,lenb);
-	}
-
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Side1 = _mm_xor_si128(Side1, Side1);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,2*e,1);
-
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,1,1);
-	Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-	R1 = _mm_insert_epi16(R1,1,0);
-	R1 = _mm_insert_epi16(R1,1,1);
-
-	for(i=2; i <= e; i++)
-	{
-		//set side
-		Side1 = _mm_slli_si128(Side1,2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_slli_si128(Down1,2);
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-
-			for(j=1;j<=i-1;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(i/2-1+(i/2-j))) != *(a-(i/2-1-(i/2-j))),0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R0 = _mm_min_epi16(R1+Side1, _mm_slli_si128(R0,2)+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down1);
-		}
-
-		else
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-			for(j=i/2-1;j>=-i/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-((i+1)/2+j-1)) != *(a-((i-1)/2-j-1)),0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down1);
-		}
-	}
-	Error = _mm_xor_si128(Error, Error);
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Error = _mm_insert_epi16(Error,e,0);
-	Side2 = _mm_insert_epi16(Side2,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Error = _mm_slli_si128(Error, 2);
-		Error = _mm_insert_epi16(Error, e, 0);
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	for(; i <= 2*lenb-(e-1);i++)
-	{
-		flag = 0;
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			for(j=e/2;j>=-e/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(i/2-1+j)) != *(a-(i/2-1-j)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			if(_mm_extract_epi16(R0,0) <= e)
-				flag = 1;
-			tmp = _mm_srli_si128(R0,2);
-			for(j=0; j <= e;j++)
-			{
-				if(_mm_extract_epi16(tmp,0) <= e)
-					flag = 1;
-				tmp = _mm_srli_si128(tmp,2);
-			}
-
-			if(flag == 0)
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			for(j=-e/2+1;j<=e/2;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-((i+1)/2-j-1)) != *(a-((i-1)/2+j-1)),0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-	}
-
-	j=0;
-	int tmpE = e;
-	for(;j<2*(e-2)+1;j++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		//set the first element
-		if(j==0)
-		{
-			for( k=0;k<=e-1;k++  )
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-
-			tmpE--;
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < e-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		else if(j%2 == 0)
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < tmpE-1;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-
-
-		else
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			tmp = _mm_srli_si128(R1,2);
-			for(k=0; k < tmpE-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		i++;
-	}
-	//Diag  
-
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, 2*e, 0);
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-2)) != *(b-(lenb-1)), 1);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,1,1);
-
-	Down1 = _mm_insert_epi16(Down1, 2*e, 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-	R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-1)) != *(b-(lenb-1)), 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-	R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	if(minError > e)
-		return -1;
-	return minError;
-}
-
-inline int backwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	int i0;
-	int i1;
-	int i2;
-	int i4;
-	int i5;
-
-	int e = 4;
-	int mismatch = errThreshold;
-
-	int minError = 2*errThreshold;
-	int index = 0;
-	int tmpValue = 0;
-
-	if(lenb <= e) 
-	{
-		return smallEditDistanceB(a,lena,b,lenb);
-	}
-
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i tmp;
-	__m128i SeqA, SeqB;
-	__m128i Result;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	SeqA = _mm_setzero_si128 ();
-	SeqB = _mm_setzero_si128 ();
-	Result = _mm_setzero_si128 ();
-	/* end initialize */
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Diag = _mm_insert_epi16(Diag,minError,0);
-
-	i0 = (a[0] != b[0]);
-	i1 = min(i0, ( *(a-1)!=*b) )+1;
-	i2 = min(i0,( a[0] != *(b-1) ) )+1;
-
-	i0 = min3( i0+ ( *(a-1)!=*(b-1) ),i1+1,i2+1);
-	i4 = min(i1, ( *(a-2)!=b[0] )+1)+1;
-	i5 = min(i2, (a[0] != *(b-2))+1)+1;
-
-	R1 = _mm_insert_epi16(R1, 3, 0);
-	R1 = _mm_insert_epi16(R1, i1, 1);
-	R1 = _mm_insert_epi16(R1, i2, 2);
-	R1 = _mm_insert_epi16(R1, 3, 3);
-
-
-	R0 = _mm_insert_epi16(R0, 4, 0);
-	R0 = _mm_insert_epi16(R0, i4, 1);
-	R0 = _mm_insert_epi16(R0, i0, 2);
-	R0 = _mm_insert_epi16(R0, i5, 3);
-	R0 = _mm_insert_epi16(R0, 4, 4);
-
-
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-	Side1 = _mm_xor_si128(Side1, Side1);
-
-	Side2 = _mm_insert_epi16(Side2,minError,0);
-	Down1 = _mm_insert_epi16(Down1,minError,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-
-	index = 0;
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Side1 = _mm_slli_si128(Side1, 2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		SeqA = _mm_slli_si128(SeqA, 2);
-		SeqB = _mm_slli_si128(SeqB, 2);
-		SeqA = _mm_insert_epi16(SeqA,*(a-index),0);
-		SeqB = _mm_insert_epi16(SeqB,*(b-index),0);
-		index++;
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,minError,0);
-
-	index = 4;
-	i = 5;
-
-	int loopEnd = 2*lenb-(e-1);
-	for(; i <= loopEnd ;i++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			SeqA = _mm_slli_si128(SeqA, 2);
-			SeqB = _mm_slli_si128(SeqB, 2);
-			SeqA = _mm_insert_epi16(SeqA,*(a-(index)),0);
-			SeqB = _mm_insert_epi16(SeqB,*(b-(index)),0);
-
-			index++;
-
-			tmp = _mm_shufflelo_epi16(SeqB,27);
-			tmp = _mm_slli_si128(tmp, 2); 
-			tmpValue = _mm_extract_epi16(tmp, 5);
-			tmp = _mm_insert_epi16(tmp, tmpValue, 0);
-
-			Result = _mm_cmpeq_epi16(SeqA, tmp);
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			if(_mm_extract_epi16(R0, 0) > errThreshold && _mm_extract_epi16(R0, 1) > errThreshold && _mm_extract_epi16(R0, 2) > errThreshold 
-					&& _mm_extract_epi16(R0, 3) > errThreshold && _mm_extract_epi16(R0, 4) > errThreshold && _mm_extract_epi16(R1, 0) > errThreshold 
-					&& _mm_extract_epi16(R1, 1) > errThreshold && _mm_extract_epi16(R1, 2) > errThreshold  && _mm_extract_epi16(R1, 3) > errThreshold)
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-
-
-	}
-
-	j=0;
-	int tmpE = e;
-	for(;j<2*(e-2)+1;j++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		//set the first element
-		if(j==0)
-		{
-			for( k=0;k<=e-1;k++  )
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < e-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		else if(j%2 == 0)
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < tmpE-1;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-
-
-		else
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			tmp = _mm_srli_si128(R1,2);
-			for(k=0; k < tmpE-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		i++;
-	}
-	//Diag  
-
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, 2*errThreshold, 0);
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-2)) != *(b-(lenb-1)), 1);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,1,1);
-
-	Down1 = _mm_insert_epi16(Down1, 2*errThreshold, 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-	R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-1)) != *(b-(lenb-1)), 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-	R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	if(minError > mismatch)
-		return -1;
-	return minError;
-}
-
-int backwardEditDistance4SSE2(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	int i0;
-	int i1;
-	int i2;
-	int i4;
-	int i5;
-
-	int e = errThreshold;
-
-	int minError = 2*e;
-	int index = 0;
-	int tmpValue = 0;
-
-	if(lenb <= e) 
-	{
-		return smallEditDistanceB(a,lena,b,lenb);
-	}
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i tmp;
-	__m128i SeqA, SeqB;
-	__m128i Result;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	SeqA = _mm_setzero_si128 ();
-	SeqB = _mm_setzero_si128 ();
-	Result = _mm_setzero_si128 ();
-	/* end initialize */
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	i0 = (a[0] != b[0]);
-	i1 = min(i0, ( *(a-1)!=*b) )+1;
-	i2 = min(i0,( a[0] != *(b-1) ) )+1;
-
-	i0 = min3( i0+ ( *(a-1)!=*(b-1) ),i1+1,i2+1);
-	i4 = min(i1, ( *(a-2)!=b[0] )+1)+1;
-	i5 = min(i2, (a[0] != *(b-2))+1)+1;
-
-	R1 = _mm_insert_epi16(R1, 3, 0);
-	R1 = _mm_insert_epi16(R1, i1, 1);
-	R1 = _mm_insert_epi16(R1, i2, 2);
-	R1 = _mm_insert_epi16(R1, 3, 3);
-
-
-	R0 = _mm_insert_epi16(R0, 4, 0);
-	R0 = _mm_insert_epi16(R0, i4, 1);
-	R0 = _mm_insert_epi16(R0, i0, 2);
-	R0 = _mm_insert_epi16(R0, i5, 3);
-	R0 = _mm_insert_epi16(R0, 4, 4);
-
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-	Side1 = _mm_xor_si128(Side1, Side1);
-
-	Side2 = _mm_insert_epi16(Side2,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-
-	index = 0;
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Side1 = _mm_slli_si128(Side1, 2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		SeqA = _mm_slli_si128(SeqA, 2);
-		SeqB = _mm_slli_si128(SeqB, 2);
-		SeqA = _mm_insert_epi16(SeqA,*(a-index),0);
-		SeqB = _mm_insert_epi16(SeqB,*(b-index),0);
-		index++;
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	index = 4;
-	i = 5;
-	int loopEnd = 2*lenb-(e-1);
-	for(; i <= loopEnd ;i++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			SeqA = _mm_slli_si128(SeqA, 2);
-			SeqB = _mm_slli_si128(SeqB, 2);
-			SeqA = _mm_insert_epi16(SeqA,*(a-(index)),0);
-			SeqB = _mm_insert_epi16(SeqB,*(b-(index)),0);
-
-			index++;
-
-			tmp = _mm_shufflelo_epi16(SeqB,27);
-			tmp = _mm_slli_si128(tmp, 2); 
-			tmpValue = _mm_extract_epi16(tmp, 5);
-			tmp = _mm_insert_epi16(tmp, tmpValue, 0);
-
-			Result = _mm_cmpeq_epi16(SeqA, tmp);
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			//tmp = _mm_sub_epi16(Error, R0);
-			//i0 = _mm_movemask_epi8(tmp);
-
-			if( _mm_extract_epi16(R0, 0) > e && _mm_extract_epi16(R0, 1) > e && _mm_extract_epi16(R0, 2) > e
-					&& _mm_extract_epi16(R0, 3) > e && _mm_extract_epi16(R0, 4) > e && _mm_extract_epi16(R1, 0) > e && 
-					_mm_extract_epi16(R1, 1) > e && _mm_extract_epi16(R1, 2) > e && _mm_extract_epi16(R1, 3) > e  )
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-
-
-	}
-
-	j=0;
-	
-	int tmpE = e;
-	
-	for(;j<2*(e-2)+1;j++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		//set the first element
-		if(j==0)
-		{
-			for( k=0;k<=e-1;k++  )
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < e-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		else if(j%2 == 0)
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < tmpE-1;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-
-
-		else
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, *(b-(lenb-1-k)) != *(a-((i-lenb)-1+k)),0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			tmp = _mm_srli_si128(R1,2);
-			for(k=0; k < tmpE-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		i++;
-	}
-	//Diag  
-
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, 2*e, 0);
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-2)) != *(b-(lenb-1)), 1);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,1,1);
-
-	Down1 = _mm_insert_epi16(Down1, 2*e, 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-	R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	Diag = _mm_insert_epi16(Diag, *(a-(lenb+e-1)) != *(b-(lenb-1)), 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-	R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	if(minError > e)
-		return -1;
-	return minError;
-}
-
-inline int forwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	int i0=0;
-	int i1=0;
-	int i2=0;
-	int i4=0;
-	int i5=0;
-
-	int mismatch = errThreshold;
-	int e = 4;
-
-	int minError = 4*mismatch+1;
-	int index = 0;
-	int tmpValue = 0;
-
-	if(lenb <= e)
-	{
-		return smallEditDistanceF(a,lena,b,lenb);
-	}
-
-
-	register __m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i tmp;
-	register __m128i SeqA, SeqB;
-	__m128i Result;
-
-	__m128i tmpSeqA;
-	__m128i tmpSeqB;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	SeqA = _mm_setzero_si128 ();
-	SeqB = _mm_setzero_si128 ();
-	Result = _mm_setzero_si128 ();
-	/* end initialize */
-
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Diag = _mm_insert_epi16(Diag,minError,0);
-
-	i0 = (a[0] != b[0]);
-	i1 = min(i0, (a[1]!=b[0]))+1;
-	i2 = min(i0,(a[0]!=b[1]))+1;
-
-	i0 = min3(i0+(a[1]!=b[1]),i1+1,i2+1);
-	i4 = min(i1, (a[2]!=b[0])+1)+1;
-	i5 = min(i2, (a[0]!=b[2])+1)+1;
-
-	R1 = _mm_insert_epi16(R1, 3, 0);
-	R1 = _mm_insert_epi16(R1, i1, 1);
-	R1 = _mm_insert_epi16(R1, i2, 2);
-	R1 = _mm_insert_epi16(R1, 3, 3);
-
-	R0 = _mm_insert_epi16(R0, 4, 0);
-	R0 = _mm_insert_epi16(R0, i4, 1);
-	R0 = _mm_insert_epi16(R0, i0, 2);
-	R0 = _mm_insert_epi16(R0, i5, 3);
-	R0 = _mm_insert_epi16(R0, 4, 4);
-
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-	Side1 = _mm_xor_si128(Side1, Side1);
-
-	Side2 = _mm_insert_epi16(Side2,minError,0);
-	Down1 = _mm_insert_epi16(Down1,minError,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-
-	index = 0;
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Side1 = _mm_slli_si128(Side1, 2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		SeqA = _mm_slli_si128(SeqA, 2);
-		SeqB = _mm_slli_si128(SeqB, 2);
-		SeqA = _mm_insert_epi16(SeqA,a[index],0);
-		SeqB = _mm_insert_epi16(SeqB,b[index],0);
-		index++;
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,minError,0);
-
-	index = 4;
-	i = 5;
-
-	int loopEnd = 2*lenb-(e-1);
-	for(; i <= loopEnd ;i++)
-	{
-		if( i%2 == 0)
-		{
-			tmpSeqA = _mm_slli_si128(SeqA, 2);
-			tmpSeqB = _mm_slli_si128(SeqB, 2);
-			SeqA = _mm_insert_epi16(tmpSeqA,a[index],0);
-			SeqB = _mm_insert_epi16(tmpSeqB,b[index],0);
-
-			index++;
-
-			tmp = _mm_shufflelo_epi16(SeqB,27);
-			tmp = _mm_slli_si128(tmp, 2); 
-			tmpValue = _mm_extract_epi16(tmp, 5);
-			tmp = _mm_insert_epi16(tmp, tmpValue, 0);
-
-			Result = _mm_cmpeq_epi16(SeqA, tmp);
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			if(_mm_extract_epi16(R0, 0) > errThreshold && _mm_extract_epi16(R0, 1) > errThreshold && _mm_extract_epi16(R0, 2) > errThreshold 
-					&& _mm_extract_epi16(R0, 3) > errThreshold && _mm_extract_epi16(R0, 4) > errThreshold && 
-					_mm_extract_epi16(R1, 0) > errThreshold && _mm_extract_epi16(R1, 1) > errThreshold && 
-					_mm_extract_epi16(R1, 2) > errThreshold && _mm_extract_epi16(R1, 3) > errThreshold)
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
-			Diag =  _mm_andnot_si128(Result, MASK);
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-	}
-
-        j=0;
-        int tmpE = e;
-        for(;j<2*(e-2)+1;j++)
-        {
-
-			Diag = _mm_xor_si128(Diag, Diag);
-			//set the first element
-			if(j==0)
-			{
-				for( k=0;k<=e-1;k++  )
-				{
-					Diag = _mm_slli_si128(Diag, 2);
-					Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-				}
-
-				R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-				R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-				tmpE--;
-
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-			else if(j%2 == 0)
-			{
-				for(k=0;k<tmpE;k++)
-				{
-					Diag = _mm_slli_si128(Diag, 2);
-					Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-				}
-
-				R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-				R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-				tmpE--;
-
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < tmpE-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-
-
-			else
-			{
-				for(k=0;k<tmpE;k++)
-				{
-					Diag = _mm_slli_si128(Diag, 2);
-					Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-				}
-
-				R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-				R1 = _mm_min_epi16(R1, R0+Down1);
-
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < tmpE-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-			i++;
-		}
-		//Diag  
-
-        Diag = _mm_xor_si128(Diag,Diag);
-        Diag = _mm_insert_epi16(Diag, minError, 0);
-        Diag = _mm_insert_epi16(Diag, a[lenb+e-2] != b[lenb-1], 1);
-
-        Side1 = _mm_insert_epi16(Side1,1,0);
-        Side1 = _mm_insert_epi16(Side1,1,1);
-
-        Down1 = _mm_insert_epi16(Down1, minError, 0);
-        Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-        R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-        R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-        minError = min(minError, _mm_extract_epi16(R1,1));
-
-        Diag = _mm_insert_epi16(Diag, a[lenb+e-1] != b[lenb-1], 0);
-        Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-        R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-        R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-
-        minError = min(minError, _mm_extract_epi16(R0,0));
-
-
-        if(minError > mismatch)
-                return -1;
-        return minError;
-}
-
-
-
-int forwardEditDistance4SSE2(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-                return 0;
-
-        int i = 0;
-        int j = 0;
-        int k = 0;
-
-        int i0=0;
-	int i1=0;
-	int i2=0;
-	int i4=0;
-	int i5=0;
-
-        int e = errThreshold;
-
-        int minError = 2*e;
-	int index = 0;
-	int tmpValue = 0;
-
-	if(lenb <= e)
-        {
-                return smallEditDistanceF(a,lena,b,lenb);
-        }
-
-
-        register __m128i R0, R1;
-        __m128i Diag;
-        __m128i Side1, Side2;
-        __m128i Down1, Down2;
-        __m128i tmp;
-	register __m128i SeqA, SeqB;
-        __m128i Result;
-
-	__m128i tmpSeqA;
-	__m128i tmpSeqB;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	SeqA = _mm_setzero_si128 ();
-	SeqB = _mm_setzero_si128 ();
-	Result = _mm_setzero_si128 ();
-	/* end initialize */
-
-        R1 = _mm_xor_si128(R1, R1);
-        R0 = _mm_xor_si128(R0, R0);
-
-        Diag = _mm_xor_si128(Diag, Diag);
-        Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	i0 = (a[0] != b[0]);
-	i1 = min(i0, (a[1]!=b[0]))+1;
-	i2 = min(i0,(a[0]!=b[1]))+1;
-
-	i0 = min3(i0+(a[1]!=b[1]),i1+1,i2+1);
-	i4 = min(i1, (a[2]!=b[0])+1)+1;
-	i5 = min(i2, (a[0]!=b[2])+1)+1;
-
-	R1 = _mm_insert_epi16(R1, 3, 0);
-        R1 = _mm_insert_epi16(R1, i1, 1);
-        R1 = _mm_insert_epi16(R1, i2, 2);
-	R1 = _mm_insert_epi16(R1, 3, 3);
-
-	R0 = _mm_insert_epi16(R0, 4, 0);
-	R0 = _mm_insert_epi16(R0, i4, 1);
-	R0 = _mm_insert_epi16(R0, i0, 2);
-	R0 = _mm_insert_epi16(R0, i5, 3);
-	R0 = _mm_insert_epi16(R0, 4, 4);
-
-        Side2 = _mm_xor_si128(Side2, Side2);
-        Down2 = _mm_xor_si128(Down2, Down2);
-        Down1 = _mm_xor_si128(Down1, Down1);
-	Side1 = _mm_xor_si128(Side1, Side1);
-
-        Side2 = _mm_insert_epi16(Side2,2*e,0);
-        Down1 = _mm_insert_epi16(Down1,2*e,0);
-		
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	
-	index = 0;
-	for(j=0; j < e; j++)
-        {
-                Side2 = _mm_slli_si128(Side2, 2);
-                Side2 = _mm_insert_epi16(Side2,1,0);
-
-                Down1 = _mm_slli_si128(Down1, 2);
-                Down1 = _mm_insert_epi16(Down1,1,0);
-
-                Down2 = _mm_slli_si128(Down2, 2);
-                Down2 = _mm_insert_epi16(Down2,1,0);
-	
-		Side1 = _mm_slli_si128(Side1, 2);
-	        Side1 = _mm_insert_epi16(Side1,1,0);
-
-		SeqA = _mm_slli_si128(SeqA, 2);
-                SeqB = _mm_slli_si128(SeqB, 2);
-                SeqA = _mm_insert_epi16(SeqA,a[index],0);
-                SeqB = _mm_insert_epi16(SeqB,b[index],0);
-                index++;
-        }
-
-        Down2= _mm_slli_si128(Down2, 2);
-        Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	index = 4;
-	i = 5;
-
-	int loopEnd = 2*lenb-(e-1);
-        for(; i <= loopEnd ;i++)
-        {
-                //Diag = _mm_xor_si128(Diag, Diag);
-                if( i%2 == 0)
-                {
-			tmpSeqA = _mm_slli_si128(SeqA, 2);
-                        tmpSeqB = _mm_slli_si128(SeqB, 2);
-                        SeqA = _mm_insert_epi16(tmpSeqA,a[index],0);
-                        SeqB = _mm_insert_epi16(tmpSeqB,b[index],0);
-
-                        index++;
-			
-			tmp = _mm_shufflelo_epi16(SeqB,27);
-			tmp = _mm_slli_si128(tmp, 2); 
-			tmpValue = _mm_extract_epi16(tmp, 5);
-			tmp = _mm_insert_epi16(tmp, tmpValue, 0);
-
-                        Result = _mm_cmpeq_epi16(SeqA, tmp);
-                        Diag =  _mm_andnot_si128(Result, MASK);
-
-                        R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-                        R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-                        if(_mm_extract_epi16(R0, 0) > e && _mm_extract_epi16(R0, 1) > e && _mm_extract_epi16(R0, 2) > e 
-				&& _mm_extract_epi16(R0, 3) > e && _mm_extract_epi16(R0, 4) > e && _mm_extract_epi16(R1, 0) > e && 
-				  _mm_extract_epi16(R1, 1) > e && _mm_extract_epi16(R1, 2) > e && _mm_extract_epi16(R1, 3) > e)
-                                return -1;
-
-	               if(i == 2*lenb-e)
-                        {
-                                tmp = _mm_srli_si128(R0,2);
-                                for(k=0; k < e-1;k++)
-                                        tmp = _mm_srli_si128(tmp,2);
-                                minError = _mm_extract_epi16(tmp,0);
-                        }
-
-                }
-
-                else
-                {
-                        Result = _mm_cmpeq_epi16(SeqA, _mm_shufflelo_epi16(SeqB,27));
-                        Diag =  _mm_andnot_si128(Result, MASK);
-
-                        R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-                        R1 = _mm_min_epi16(R1, R0+Down1);
-
-                        if(i >= 2*lenb-e)
-                        {
-                                tmp = _mm_srli_si128(R1,2);
-                                for(k=0; k < e-2;k++)
-                                        tmp = _mm_srli_si128(tmp,2);
-                                minError = min(minError, _mm_extract_epi16(tmp,0));
-                        }
-                }
-
-
-	}
-        j=0;
-        int tmpE = e;
-        for(;j<2*(e-2)+1;j++)
-        {
-
-                Diag = _mm_xor_si128(Diag, Diag);
-                //set the first element
-                if(j==0)
-                {
-                        for( k=0;k<=e-1;k++  )
-                        {
-                                Diag = _mm_slli_si128(Diag, 2);
-                                Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-                        }
-
-                        R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-                        R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-                        tmpE--;
-
-                        tmp = _mm_srli_si128(R0,2);
-                        for(k=0; k < e-2;k++)
-                                tmp = _mm_srli_si128(tmp,2);
-                        minError = min(minError, _mm_extract_epi16(tmp,0));
-                }
-		else if(j%2 == 0)
-                {
-                        for(k=0;k<tmpE;k++)
-                        {
-                                Diag = _mm_slli_si128(Diag, 2);
-                                Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-                        }
-
-                        R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-                        R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-                        tmpE--;
-
-                        tmp = _mm_srli_si128(R0,2);
-                        for(k=0; k < tmpE-1;k++)
-                                tmp = _mm_srli_si128(tmp,2);
-                        minError = min(minError, _mm_extract_epi16(tmp,0));
-                }
-
-
-		else
-                {
-                        for(k=0;k<tmpE;k++)
-                        {
-                                Diag = _mm_slli_si128(Diag, 2);
-                                Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-                        }
-
-                        R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-                        R1 = _mm_min_epi16(R1, R0+Down1);
-
-                        tmp = _mm_srli_si128(R1,2);
-                        for(k=0; k < tmpE-2;k++)
-                                tmp = _mm_srli_si128(tmp,2);
-                        minError = min(minError, _mm_extract_epi16(tmp,0));
-                }
-                i++;
-        }
- 	//Diag  
-
-        Diag = _mm_xor_si128(Diag,Diag);
-        Diag = _mm_insert_epi16(Diag, 2*e, 0);
-        Diag = _mm_insert_epi16(Diag, a[lenb+e-2] != b[lenb-1], 1);
-
-        Side1 = _mm_insert_epi16(Side1,1,0);
-        Side1 = _mm_insert_epi16(Side1,1,1);
-
-        Down1 = _mm_insert_epi16(Down1, 2*e, 0);
-        Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-        R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-        R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-        minError = min(minError, _mm_extract_epi16(R1,1));
-
-        Diag = _mm_insert_epi16(Diag, a[lenb+e-1] != b[lenb-1], 0);
-        Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-        R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-        R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-        minError = min(minError, _mm_extract_epi16(R0,0));
-
-        if(minError > e)
-                return -1;
-        return minError;
-}
-
-int forwardEditDistanceSSE2Odd(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	int e = errThreshold;
-
-	int minError = 2*e;
-
-	char flag = 0;
-
-	if(lenb <= e)
-	{
-		return smallEditDistanceF(a,lena,b,lenb);
-	}
-
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i Error;
-	__m128i tmp;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Error = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Side1 = _mm_xor_si128(Side1, Side1);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,2*e,1);
-
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,1,1);
-	Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-	R1 = _mm_insert_epi16(R1,1,0);
-	R1 = _mm_insert_epi16(R1,1,1);
-
-	for(i=2; i <= e; i++)
-	{
-		//set side
-		Side1 = _mm_slli_si128(Side1,2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_slli_si128(Down1,2);
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-
-			for(j=1;j<=i-1;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[i/2-1+(i/2-j)] != a[i/2-1-(i/2-j)],0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R0 = _mm_min_epi16(R1+Side1, _mm_slli_si128(R0,2)+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down1);
-
-		}
-
-		else
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-			for(j=i/2-1;j>=-i/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[(i+1)/2+j-1] != a[(i-1)/2-j-1],0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down1);
-
-		}
-	}
-	Error = _mm_xor_si128(Error, Error);
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Side1 = _mm_xor_si128(Side1, Side1);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-
-	Error = _mm_insert_epi16(Error,e,0);
-	Side2 = _mm_insert_epi16(Side2,2*e,0);
-	Side1 = _mm_insert_epi16(Side2,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Side1 = _mm_slli_si128(Side1, 2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Error = _mm_slli_si128(Error, 2);
-		Error = _mm_insert_epi16(Error, e, 0);
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	for(; i <= 2*lenb-(e-1);i++)
-	{
-		flag = 0;
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			for(j=e/2;j>=-e/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[i/2-1+j] != a[i/2-1-j],0);
-			}
-
-
-			R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-			R0 = _mm_min_epi16(R0, R1+Down1);
-
-			if(_mm_extract_epi16(R0,0) <= e)
-				flag = 1;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(j=0; j < e-1;j++)
-			{
-				if(_mm_extract_epi16(tmp,0) <= e)
-					flag = 1;
-				tmp = _mm_srli_si128(tmp,2);
-			}
-			//			printf("#%d %d %d\n", _mm_extract_epi16(R0,0), _mm_extract_epi16(R0,1), _mm_extract_epi16(R0,2));	
-			if(flag == 0)
-				return -1;
-
-			if(i == 2*lenb-(e-1))
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			for(j=e/2;j>=-e/2-1;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[(i+1)/2+j-1] != a[(i)/2-j-1],0);
-			}
-
-			R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-			//printf("#%d %d %d %d\n", _mm_extract_epi16(R1,0), _mm_extract_epi16(R1,1), _mm_extract_epi16(R1,2),
-			//	_mm_extract_epi16(R1,3));    
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-	}
-
-	//first cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, b[lenb-3] != a[lena], 0);
-	Diag = _mm_insert_epi16(Diag, b[lenb-2] != a[lena-1], 1);
-	Diag = _mm_insert_epi16(Diag, b[lenb-1] != a[lena-2], 2);
-	Diag = _mm_insert_epi16(Diag, 2*e, 3);
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-
-	minError = min(minError, _mm_extract_epi16(R1,2));
-
-	//second cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, b[lenb-2] != a[lena], 0);
-	Diag = _mm_insert_epi16(Diag, b[lenb-1] != a[lena-1], 1);
-	Diag = _mm_insert_epi16(Diag, 2*e, 2);
-
-	R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0, R1+Down1);
-
-
-	minError = min(minError, _mm_extract_epi16(R0,1));
-
-	//third cell
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, b[lenb-2] != a[lena+1], 0);
-	Diag = _mm_insert_epi16(Diag, b[lenb-1] != a[lena], 1);
-	Diag = _mm_insert_epi16(Diag, 2*e, 2);
-
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	//forth
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, b[lenb-1] != a[lena+1], 0);
-	Diag = _mm_insert_epi16(Diag, 2*e, 1);
-
-	R0 = _mm_min_epi16(_mm_srli_si128(R1,2)+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0, R1+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	//fifth
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, b[lenb-1] != a[lena+2], 0);
-	Diag = _mm_insert_epi16(Diag, 2*e, 1);
-
-	R1 = _mm_min_epi16(R0+Side2, R1+Diag);
-	R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down2);
-
-
-	minError = min(minError, _mm_extract_epi16(R1,0));
-
-	if(minError > e)
-		return -1;
-	return minError;
-
-}
-
-int forwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-		return 0;
-
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	int e = errThreshold;
-
-	int minError = 2*e;
-
-	char flag = 0;
-	
-	if(lenb <= e)
-	{
-		return smallEditDistanceF(a,lena,b,lenb);
-	}
-
-
-	__m128i R0, R1;
-	__m128i Diag;
-	__m128i Side1, Side2;
-	__m128i Down1, Down2;
-	__m128i Error;
-	__m128i tmp;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Error = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	R1 = _mm_xor_si128(R1, R1);
-	R0 = _mm_xor_si128(R0, R0);
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Side1 = _mm_xor_si128(Side1, Side1);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,2*e,1);
-
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,1,1);
-	Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-	R1 = _mm_insert_epi16(R1,1,0);
-	R1 = _mm_insert_epi16(R1,1,1);
-
-	for(i=2; i <= e; i++)
-	{
-		//set side
-		Side1 = _mm_slli_si128(Side1,2);
-		Side1 = _mm_insert_epi16(Side1,1,0);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_slli_si128(Down1,2);
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-
-			for(j=1;j<=i-1;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[i/2-1+(i/2-j)] != a[i/2-1-(i/2-j)],0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R0 = _mm_min_epi16(R1+Side1, _mm_slli_si128(R0,2)+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down1);
-		}
-
-		else
-		{
-			Diag = _mm_insert_epi16(Diag,2*e,0);
-			for(j=i/2-1;j>=-i/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[(i+1)/2+j-1] != a[(i-1)/2-j-1],0);
-			}
-			Diag = _mm_slli_si128(Diag, 2);
-			Diag = _mm_insert_epi16(Diag, 2*e,0);
-
-			R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-			R1 = _mm_min_epi16(R1,  _mm_slli_si128(R0,2)+Down1);
-		}
-	}
-	Error = _mm_xor_si128(Error, Error);
-	Side2 = _mm_xor_si128(Side2, Side2);
-	Down2 = _mm_xor_si128(Down2, Down2);
-	Down1 = _mm_xor_si128(Down1, Down1);
-
-	Error = _mm_insert_epi16(Error,e,0);
-	Side2 = _mm_insert_epi16(Side2,2*e,0);
-	Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-
-	for(j=0; j < e; j++)
-	{
-		Side2 = _mm_slli_si128(Side2, 2);
-		Side2 = _mm_insert_epi16(Side2,1,0);
-
-		Down1 = _mm_slli_si128(Down1, 2);
-		Down1 = _mm_insert_epi16(Down1,1,0);
-
-		Down2 = _mm_slli_si128(Down2, 2);
-		Down2 = _mm_insert_epi16(Down2,1,0);
-
-		Error = _mm_slli_si128(Error, 2);
-		Error = _mm_insert_epi16(Error, e, 0);
-	}
-
-	Down2= _mm_slli_si128(Down2, 2);
-	Down2 = _mm_insert_epi16(Down2,2*e,0);
-
-	for(; i <= 2*lenb-(e-1);i++)
-	{
-		flag = 0;
-		Diag = _mm_xor_si128(Diag, Diag);
-		if( i%2 == 0)
-		{
-			for(j=e/2;j>=-e/2;j--)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[i/2-1+j] != a[i/2-1-j],0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-
-			if(_mm_extract_epi16(R0,0) <= e)
-				flag = 1;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(j=0; j < e-1;j++)
-			{
-				if(_mm_extract_epi16(tmp,0) <= e)
-					flag = 1;
-				tmp = _mm_srli_si128(tmp,2);
-			}
-
-			
-			if(flag == 0)
-				return -1;
-
-			if(i == 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R0,2);
-				for(k=0; k < e-1;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = _mm_extract_epi16(tmp,0);
-			}
-
-		}
-
-		else
-		{
-			for(j=-e/2+1;j<=e/2;j++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[(i+1)/2-j-1] != a[(i-1)/2+j-1],0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			if(i >= 2*lenb-e)
-			{
-				tmp = _mm_srli_si128(R1,2);
-				for(k=0; k < e-2;k++)
-					tmp = _mm_srli_si128(tmp,2);
-				minError = min(minError, _mm_extract_epi16(tmp,0));
-			}
-		}
-	}
-
-	j=0;
-	int tmpE = e;
-	for(;j<2*(e-2)+1;j++)
-	{
-
-		Diag = _mm_xor_si128(Diag, Diag);
-		//set the first element
-		if(j==0)
-		{
-			for( k=0;k<=e-1;k++  )
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < e-2;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		else if(j%2 == 0)
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-			}
-
-			R0 = _mm_min_epi16(R1+Side2, R0+Diag);
-			R0 = _mm_min_epi16(R0, _mm_slli_si128(R1,2)+Down2);
-
-			tmpE--;
-
-			tmp = _mm_srli_si128(R0,2);
-			for(k=0; k < tmpE-1;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-
-
-		else
-		{
-			for(k=0;k<tmpE;k++)
-			{
-				Diag = _mm_slli_si128(Diag, 2);
-				Diag = _mm_insert_epi16(Diag, b[lenb-1-k] != a[(i-lenb)-1+k],0);
-			}
-
-			R1 = _mm_min_epi16(_mm_srli_si128(R0,2)+Side1, R1+Diag);
-			R1 = _mm_min_epi16(R1, R0+Down1);
-
-			tmp = _mm_srli_si128(R1,2);
-			for(k=0; k < tmpE-1;k++)
-				tmp = _mm_srli_si128(tmp,2);
-			minError = min(minError, _mm_extract_epi16(tmp,0));
-		}
-		i++;
-	}
-	//Diag  
-
-	Diag = _mm_xor_si128(Diag,Diag);
-	Diag = _mm_insert_epi16(Diag, 2*e, 0);
-	Diag = _mm_insert_epi16(Diag, a[lenb+e-2] != b[lenb-1], 1);
-
-	Side1 = _mm_insert_epi16(Side1,1,0);
-	Side1 = _mm_insert_epi16(Side1,1,1);
-
-	Down1 = _mm_insert_epi16(Down1, 2*e, 0);
-	Down1 = _mm_insert_epi16(Down1, 1, 1);
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-	R1 = _mm_min_epi16(R1, _mm_slli_si128(R0,2)+Down1);
-
-	minError = min(minError, _mm_extract_epi16(R1,1));
-
-	Diag = _mm_insert_epi16(Diag, a[lenb+e-1] != b[lenb-1], 1);
-	Down1 = _mm_insert_epi16(Down1, 1, 0);
-
-	R0 = _mm_min_epi16(R1+Down1,R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_srli_si128(R1,2)+Side1);
-
-	minError = min(minError, _mm_extract_epi16(R0,0));
-
-	if(minError > e)
-		return -1;
-	return minError;
-}
-
-
-int forwardEditDistance2SSE2(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-                return 0;
-	
-		
-
-        int i0 = 0;
-        int i1 = 0;
-
-
-        int error;                      //0: if the two character are equal 1: if not
-
-        int i = 0;                      //loop index
-
-        int e = 2;                      //error bound
-
-	int totalError = 0;
-
-        __m128i R0;
-        __m128i R1;
-
-        __m128i Side1, Side2,Side;                    //side matrix
-        __m128i Down1, Down2,Down;                    //down matrix
-        __m128i Diag; 
-
-        __m128i tmp;
-	__m128i ERROR_REACH;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Side = _mm_setzero_si128 ();
-        Down = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-        ERROR_REACH = _mm_setzero_si128 ();
-	/* end initialize */
-
-
-	if(lenb <= e)
-        {
-                return smallEditDistanceF(a,lena,b,lenb);
-        }
-	
-	ERROR_REACH = _mm_set_epi16(0,0,0,0,0,e,e,e);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-        R1 = _mm_insert_epi16(R1,1,0);
-        R1 = _mm_insert_epi16(R1,1,1);
-
-//        error = ((a[0]) != (b[0]));
-
-	Diag  = _mm_set_epi16(0,0,0,0,0,2*e,((a[0]) != (b[0])),2*e);
-	Side1 = _mm_set_epi16(0,0,0,0,0,2*e,1,1);
-	Side2 = _mm_set_epi16(0,0,0,0,0,1,1,2*e);
-	Down1 = _mm_set_epi16(0,0,0,0,0,2*e,1,1);
-	Down2 = _mm_set_epi16(0,0,0,0,0,1,1,2*e);
-
-        tmp = _mm_slli_si128(R1,2);
-
-        R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-        R0 = _mm_min_epi16(R0,tmp+Down2);
-
-	for (i = 3; i  < 2*lena; i++)
-        {
-                if(i % 2 ==1)
-                {
-                        
-			Diag = _mm_xor_si128(Diag, Diag);
-                        error = ((a[(i+1)/2-1]) != (b[(i-1)/2-1]));
-                        Diag = _mm_insert_epi16(Diag,error,0);
-                        error = ((a[(i-1)/2-1]) != (b[(i+1)/2-1]));
-                        Diag = _mm_insert_epi16(Diag,error,1);
-//		        Diag  = _mm_set_epi16(0, 0, 0, 0, 0, 0, ((a[(i-1)/2-1]) != (b[(i+1)/2-1])) ,((a[(i+1)/2-1]) != (b[(i-1)/2-1])));
-
-
-                        tmp = _mm_srli_si128(R0,2);
-
-                        R1 = _mm_min_epi16(tmp+Side1, R1+Diag);
-                        R1 = _mm_min_epi16(R1,R0+Down1);           
-
-                        if(i > 2 * lenb - 2)
-			{
-	                        i1 = _mm_extract_epi16(R1, 1);
-                                totalError = min(totalError, i1);                          
-			}
-                }
-
-		else if(i % 2 == 0)
-                {
-                        error = ((a[i/2]) != (b[i/2-2]));
-                        Diag = _mm_insert_epi16(Diag,error,0);
-                        error = ((a[i/2-1]) != (b[i/2-1]));
-                        Diag = _mm_insert_epi16(Diag,error,1);
-                        error = ((a[i/2-2]) != (b[i/2]));
-                        Diag = _mm_insert_epi16(Diag,error,2);
-
-        //                Diag  = _mm_set_epi16(0, 0, 0, 0, 0, ((a[i/2-2]) != (b[i/2])) , ((a[i/2-1]) != (b[i/2-1]))  , ((a[i/2]) != (b[i/2-2])) );
-		
-                        tmp = _mm_slli_si128(R1,2);
-
-                        R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-                        R0 = _mm_min_epi16(R0,tmp+Down2);
-
-			tmp = _mm_sub_epi16(ERROR_REACH, R0);
-                        i0 = _mm_movemask_epi8(tmp);
-
-                        if(i0 == 63 &&  _mm_extract_epi16(R1,0) > errThreshold  && _mm_extract_epi16(R1,1) > errThreshold && i < 2 * lenb - 2)
-                                return -1;
-                        if(i == 2 * lenb - 2) {
-				totalError = _mm_extract_epi16(R0, 2);                       
-			}
-                }
-        }
-	
-        Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-	//fill the first part of the error
-	error = ((a[i/2]) != (b[i/2-2]));
-        Diag = _mm_insert_epi16(Diag,error,0);
-	error = ((a[i/2-1]) != (b[i/2-1]));
-	Diag = _mm_insert_epi16(Diag,error,1);
-	Diag = _mm_insert_epi16(Diag,2*e,2);
-//        Diag  = _mm_set_epi16(0, 0, 0, 0, 0, 2*e , ((a[i/2-1]) != (b[i/2-1]))  , ((a[i/2]) != (b[i/2-2])) );
-
-	R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_slli_si128(R1,2)+Down1);
-
-//	i0 = _mm_extract_epi16(R0, 0);
-	i1 = _mm_extract_epi16(R0, 1);
-
-	totalError = min(totalError, i1);
-
-	//fill the second part of the error
-	i++;
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-	error = ((a[i/2]) != (b[lenb-1]));
-        Diag = _mm_insert_epi16(Diag,error,1);
-	Diag = _mm_insert_epi16(Diag,2*e,2);
-//        Diag  = _mm_set_epi16(0, 0, 0, 0, 0, 2*e , ((a[i/2]) != (b[lenb-1]))  , 2*e );
-
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-        R1 = _mm_min_epi16(R1,_mm_slli_si128(R0,2)+Down1);
-
-//        i0 = _mm_extract_epi16(R1, 0);
-        i1 = _mm_extract_epi16(R1, 1);
-
-        totalError = min(totalError, i1);
-	//fill the last the last element of the matrix
-	i++;
-
-	Diag = _mm_xor_si128(Diag, Diag);
-	error = ((a[i/2]) != (b[lenb-1]));
-        Diag = _mm_insert_epi16(Diag,error,0);
-
-//        Diag  = _mm_set_epi16(0, 0, 0, 0, 0, 0 , 0  , ((a[i/2]) != (b[lenb-1])) );
-
-
-        Down = _mm_insert_epi16(Down,1,0);
-
-        Side = _mm_insert_epi16(Side,1,0);
-
-        tmp = _mm_srli_si128(R1,2);
-
-        R0 = _mm_min_epi16(R1+Down, _mm_srli_si128(R0,2)+Diag);
-        R0 = _mm_min_epi16(R0,tmp+Side);
-
-        i0 = _mm_extract_epi16(R0, 0);
-
-        totalError = min(totalError, i0);
-
-	if(totalError > e)
-		return -1;
-        
-	return totalError;
-
-}
-
-int backwardEditDistance2SSE2(char *a, int lena, char *b,int lenb)
-{
-	if(lenb == 0 || lena == 0)
-                return 0;
-
-        int i0 = 0;
-        int i1 = 0;
-
-        int error;                      //0: if the two character are equal 1: if not
-
-        int i = 0;                      //loop index
-
-        int e = 2;                      //error bound
-
-	int totalError = 0;
-
-        __m128i R0;
-        __m128i R1;
-
-        __m128i Side1, Side2,Side;                    //side matrix
-        __m128i Down1, Down2,Down;                    //down matrix
-        __m128i Diag;                   	      //diag matrix
-
-        __m128i tmp;
-	__m128i ERROR_REACH;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Side = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-	Down = _mm_setzero_si128 ();
-	ERROR_REACH = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	if(lenb <= e) 
-        {
-                return smallEditDistanceB(a,lena,b,lenb);
-        }
-
-
-	ERROR_REACH = _mm_set_epi16(0,0,0,0,0,e,e,e);
-
-	R0 = _mm_insert_epi16(R0,0,0);
-
-        R1 = _mm_insert_epi16(R1,1,0);
-        R1 = _mm_insert_epi16(R1,1,1);
-
-        error = ((a[0]) != (b[0]));
-
-        Diag = _mm_insert_epi16(Diag,2*e,0);
-        Diag = _mm_insert_epi16(Diag,error,1);
-        Diag = _mm_insert_epi16(Diag,2*e,2);
-
-        Side1 = _mm_insert_epi16(Side1,1,0);
-        Side1 = _mm_insert_epi16(Side1,1,1);
-        Side1 = _mm_insert_epi16(Side1,2*e,2);
-
-        Side2 = _mm_insert_epi16(Side2,2*e,0);
-        Side2 = _mm_insert_epi16(Side2,1,1);
-        Side2 = _mm_insert_epi16(Side2,1,2);
-
-	Down1 = _mm_insert_epi16(Down1,1,0);
-        Down1 = _mm_insert_epi16(Down1,1,1);
-        Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-        Down2 = _mm_insert_epi16(Down2,2*e,0);
-        Down2 = _mm_insert_epi16(Down2,1,1);
-        Down2 = _mm_insert_epi16(Down2,1,2);
-
-        tmp = _mm_slli_si128(R1,2);
-
-        R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-        R0 = _mm_min_epi16(R0,tmp+Down2);
-
-//        printf("%d %d %d\n", _mm_extract_epi16(R0,0), _mm_extract_epi16(R0,1), _mm_extract_epi16(R0,2));	
-	for (i = 3; i  < 2*lena; i++)
-        {
-                if(i % 2 ==1)
-                {
-                        Diag = _mm_sub_epi8(Diag, Diag);
-                        error = ( *(a-((i+1)/2-1)) != *(b-((i-1)/2-1)) );
-                        Diag = _mm_insert_epi16(Diag,error,0);
-                        error = ( *(a-((i-1)/2-1)) != *(b-((i+1)/2-1)) );
-                        Diag = _mm_insert_epi16(Diag,error,1);
-			//printf("#%d #%d\n", _mm_extract_epi16(Diag,0), _mm_extract_epi16(Diag,1));
-                        tmp = _mm_srli_si128(R0,2);
-
-                        R1 = _mm_min_epi16(tmp+Side1, R1+Diag);
-                        R1 = _mm_min_epi16(R1,R0+Down1);
-             
-                        if(i > 2 * lenb - 2) {			
-	                        i1 = _mm_extract_epi16(R1, 1);
-                                totalError = min(totalError, i1);                          
-			}
-//			printf("%d %d\n", _mm_extract_epi16(R1,0), _mm_extract_epi16(R1,1));
-                }
-
-		else if(i % 2 == 0)
-                {
-                        error = ( *(a-(i/2))   != *(b-(i/2-2)) );
-                        Diag = _mm_insert_epi16(Diag,error,0);
-                        error = ( *(a-(i/2-1)) != *(b-(i/2-1)) );
-                        Diag = _mm_insert_epi16(Diag,error,1);
-                        error = ( *(a-(i/2-2))    != *(b-(i/2)));
-                        Diag = _mm_insert_epi16(Diag,error,2);
-
-                        tmp = _mm_slli_si128(R1,2);
-
-                        R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-                        R0 = _mm_min_epi16(R0,tmp+Down2);
-
-			tmp = _mm_sub_epi16(ERROR_REACH, R0);
-			i0 = _mm_movemask_epi8(tmp);
-
-                        if(i0 == 63 && _mm_extract_epi16(R1,0) > errThreshold && _mm_extract_epi16(R1,1) > errThreshold && i < 2 * lenb - 2)
-                                return -1;
-
-                        if(i == 2 * lenb - 2) {
-				totalError = _mm_extract_epi16(R0, 2);
-			}                       
-                }
-        }
-        Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-	//fill the first part of the error
-	error = ( *(a-(i/2))  != *(b-(i/2-2)) );
-        Diag = _mm_insert_epi16(Diag,error,0);
-	error = ( *(a-(i/2-1)) != *(b-(i/2-1)) );
-	Diag = _mm_insert_epi16(Diag,error,1);
-	Diag = _mm_insert_epi16(Diag,2*e,2);
-
-	R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-	R0 = _mm_min_epi16(R0,_mm_slli_si128(R1,2)+Down1);
-	
-	i0 = _mm_extract_epi16(R0, 0);
-	i1 = _mm_extract_epi16(R0, 1);
-
-	totalError = min(totalError, i1);
-
-	//fill the second part of the error
-	i++;
-	Diag = _mm_sub_epi8(Diag, Diag);
-	Diag = _mm_insert_epi16(Diag,2*e,0);
-	error = ( *(a-(i/2)) != *(b-(lenb-1)) );
-        Diag = _mm_insert_epi16(Diag,error,1);
-	Diag = _mm_insert_epi16(Diag,2*e,2);
-
-	R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-        R1 = _mm_min_epi16(R1,_mm_slli_si128(R0,2)+Down1);
-
-        i0 = _mm_extract_epi16(R1, 0);
-        i1 = _mm_extract_epi16(R1, 1);
-
-        totalError = min(totalError, i1);
-
-	//fill the last the last element of the matrix
-	i++;
-	Diag = _mm_sub_epi8(Diag, Diag);
-	error = ( *(a-(i/2)) != *(b-(lenb-1)) );
-        Diag = _mm_insert_epi16(Diag,error,0);
-
-        Down = _mm_insert_epi16(Down,1,0);
-
-        Side = _mm_insert_epi16(Side,1,0);
-
-        tmp = _mm_srli_si128(R1,2);
-
-        R0 = _mm_min_epi16(R1+Down, _mm_srli_si128(R0,2)+Diag);
-        R0 = _mm_min_epi16(R0,tmp+Side);
-
-        i0 = _mm_extract_epi16(R0, 0);
-
-        totalError = min(totalError, i0);
-
-	if(totalError > e || totalError == 0)
-		return -1;
-        return totalError;
-}
-
-void initBestMapping(int totalReadNumber)
-{
-	int i = 0;
-	bestHitMappingInfo = getMem(totalReadNumber * sizeof(BestFullMappingInfo));
-	for(i = 0; i < totalReadNumber; i++) {
-		bestHitMappingInfo[i].loc = -1;
-	}
-} 
-
-
-void finalizeBestSingleMapping() 
-{
-	int i = 0;
-	char *_tmpQual, *_tmpSeq;
-	char rqual[SEQ_LENGTH + 1];
-	rqual[SEQ_LENGTH]='\0';
-
-	for(i = 0; i < _msf_seqListSize; i++)
-	{
-		if(_msf_seqList[i].hits[0] != 0)
-		{		
-			if (bestHitMappingInfo[i].dir)
-			{
-				reverse(_msf_seqList[i].qual, rqual, SEQ_LENGTH);
-				_tmpQual = rqual;
-				_tmpSeq = _msf_seqList[i].rseq;
-			}
-			else
-			{
-				_tmpQual = _msf_seqList[i].qual;
-				_tmpSeq = _msf_seqList[i].seq;
-			}
-
-
-			_msf_output.QNAME               = _msf_seqList[i].name;
-			_msf_output.FLAG                = 16 * bestHitMappingInfo[i].dir;
-			_msf_output.RNAME               = bestHitMappingInfo[i].chr;
-
-			_msf_output.POS                 = bestHitMappingInfo[i].loc;
-			_msf_output.MAPQ                = 255;
-			_msf_output.CIGAR               = bestHitMappingInfo[i].cigar ;
-			_msf_output.MRNAME              = "*";
-			_msf_output.MPOS                = 0;
-			_msf_output.ISIZE               = 0;
-
-
-			_msf_output.SEQ                 = _tmpSeq;
-			_msf_output.QUAL                = _tmpQual;
-
-			_msf_output.optSize             = 2;
-			_msf_output.optFields   = _msf_optionalFields;
-
-			_msf_optionalFields[0].tag = "NM";
-			_msf_optionalFields[0].type = 'i';
-			_msf_optionalFields[0].iVal = bestHitMappingInfo[i].err;
-
-			_msf_optionalFields[1].tag = "MD";
-			_msf_optionalFields[1].type = 'Z';
-			_msf_optionalFields[1].sVal = bestHitMappingInfo[i].md;
-
-			output(_msf_output);
-		}
-	}
-	freeMem(bestHitMappingInfo, _msf_seqListSize * sizeof(FullMappingInfo));
-}
-/**********************************************/
-int compare (const void *a, const void *b)
-{
-	return ((Pair *)a)->hv - ((Pair *)b)->hv;
-	/*char *s1 = ((Pair *)a)->hv;
-	char *s2 = ((Pair *)b)->hv;
-	int i = 0;
-	
-	int diff = 0;	
-	int sign = 0;
-
-	for(i = 0; i < SEQ_LENGTH; i++)
-	{
-		diff += (s1[i] != s2[i]);
-		if(s1[i] > s2[i])
-			sign++;
-		else if(s1[i] < s2[i])
-			sign--;
-	}
-
-	return diff*sign;*/
-//	return strncmp(s1, s2,SEQ_LENGTH);
-
-}
-/**********************************************/
-void preProcessReads()
-{
-	int i = 0;
-
-	_msf_sort_seqList = getMem(_msf_seqListSize * sizeof(Pair));
-	for(i = 0; i < _msf_seqListSize; i++)
-	{
-		_msf_sort_seqList[i].hv = hashVal(_msf_seqList[i].seq);	
-
-		_msf_sort_seqList[i].readNumber = i;
-	}
-
-	qsort(_msf_sort_seqList, _msf_seqListSize, sizeof(Pair), compare);
-
-	/*
-	for(i = 0; i < _msf_seqListSize; i++)
-        {
-		//printf("%s\n", _msf_sort_seqList[i].hv);
-	}
-	*/
-
-	_msf_map_sort_seqList = getMem(_msf_seqListSize * sizeof(int));
-
-	for(i = 0; i < _msf_seqListSize; i++)
-		_msf_map_sort_seqList[_msf_seqList[i].readNumber] = i; 	
-
-}
-/**********************************************/
-
-int verifySingleEnd(int index, char* seq, int offset)
-{
-	int curOff = 0;
-	int i;
-
-	char *ref;
-	
-	int err;
-	int errCnt =0;
-	int errCntOff = 0;
-	int NCntOff = 0;
-
-	ref = _msf_refGen + index - 1;
-
-	verificationCnt++;
-
-	for (i = 0; i < SEQ_LENGTH; i++)
-	{
-		err	= *ref != *seq;
-		errCnt += err;
-		if (errCnt > errThreshold)
-		{
-
-			return -1;
-		}
-
-		if (i >= _msf_samplingLocs[curOff] && i <= _msf_samplingLocsEnds[curOff])
-		{
-			errCntOff +=  err;
-			NCntOff += (*seq == 'N');
-		}
-		else if (curOff < _msf_samplingLocsSize && i>=_msf_samplingLocs[curOff+1])
-		{
-
-			if (errCntOff == 0 && NCntOff == 0 && offset > curOff)
-			{
-				return -1;
-			}
-
-			errCntOff = 0;
-			NCntOff = 0;
-			curOff++;
-
-			if ( i >= _msf_samplingLocs[curOff])
-			{
-				errCntOff += err;
-				NCntOff += (*seq == 'N');
-			}
-		}
-
-		ref++;
-		seq++;
-	}
-	return errCnt;
-}
-
-/*********************************************/
-void initFAST(Read *seqList, int seqListSize, int *samplingLocs, int samplingLocsSize, char *genFileName)
-{
-	int i;
-
-	if (_msf_optionalFields == NULL)
-	{
-		_msf_op = getMem(SEQ_LENGTH);
-		if (pairedEndMode)
-		{
-			_msf_optionalFields = getMem(8*sizeof(OPT_FIELDS));
-		}
-		else
-		{
-			_msf_optionalFields = getMem(2*sizeof(OPT_FIELDS));
-		}
-
-		for (i=0; i<200;i++)
-		{
-			sprintf(_msf_numbers[i],"%d%c",i, '\0');
-		}
-		sprintf(_msf_cigar, "%dM", SEQ_LENGTH);
-	}
-
-	if (_msf_samplingLocsEnds == NULL)
-	{
-		_msf_samplingLocs = samplingLocs;
-		_msf_samplingLocsSize = samplingLocsSize;
-
-		_msf_samplingLocsEnds = getMem(sizeof(int)*_msf_samplingLocsSize);
-		for (i=0; i<_msf_samplingLocsSize; i++)
-		{
-			_msf_samplingLocsEnds[i]=_msf_samplingLocs[i]+WINDOW_SIZE-1;
-		}
-
-		_msf_seqList = seqList;
-		_msf_seqListSize = seqListSize;
-
-		preProcessReads();
-
-		_msf_oeaMapping = getMem(_msf_seqListSize * sizeof(int));
-		for(i = 0; i < _msf_seqListSize; i++)
-		{
-			_msf_oeaMapping[i] = 0;
-		}
-
-		_msf_discordantMapping = getMem(_msf_seqListSize * sizeof(int));
-		for(i = 0; i < _msf_seqListSize; i++)
-		{
-			_msf_discordantMapping[i] = 0;
-		}
-
-	}
-
-	if (_msf_refGenName == NULL)
-	{
-		_msf_refGenName = getMem(4*SEQ_LENGTH);
-	}
-	_msf_refGen =  getRefGenome();
-	_msf_refGenLength = strlen(_msf_refGen);
-
-	_msf_refGenOffset = getRefGenomeOffset();
-	snprintf(_msf_refGenName, 4*SEQ_LENGTH,"%s%c", getRefGenomeName(), '\0');
-	_msf_refGenName[strlen(getRefGenomeName())] = '\0';
-
-	
-	if (_msf_verifiedLocs != NULL){
-		freeMem(_msf_verifiedLocs, sizeof(int) * (_msf_refGenLength+1));
-	}
-
-	_msf_verifiedLocs = (int *) getMem(sizeof(int)*(_msf_refGenLength+1));
-
-	for (i=0; i<=_msf_refGenLength; i++)
-		_msf_verifiedLocs[i] = _msf_seqListSize*10+1;
-
-      
-	
-	if (pairedEndMode && _msf_seqHits == NULL)
-	{
-
-		_msf_mappingInfo  = getMem(seqListSize * sizeof (MappingInfo));
-		
-		for (i=0; i<seqListSize; i++)
-		{
-			//_msf_mappingInfo[i].next = getMem(sizeof(MappingLocations));
-			_msf_mappingInfo[i].next = NULL;
-			_msf_mappingInfo[i].size = 0;
-		}
-
-		_msf_seqHits = getMem((_msf_seqListSize) * sizeof(int));
-
-
-		for (i=0; i<_msf_seqListSize; i++)
-		{
-			_msf_seqHits[i] = 0;
-		}
-
-		_msf_readHasConcordantMapping = getMem(_msf_seqListSize / 2 * sizeof(char));
-		for(i = 0; i < _msf_seqListSize/2; i++)
-		{
-			_msf_readHasConcordantMapping[i] = 0;
-		}
-
-		initLoadingRefGenome(genFileName);
-	}
-
-	if (_msf_refGenOffset == 0)
-	{
-		_msf_refGenBeg = 1;
-	}
-	else
-	{
-		_msf_refGenBeg = CONTIG_OVERLAP - SEQ_LENGTH + 2;
-	}
-	_msf_refGenEnd = _msf_refGenLength - SEQ_LENGTH + 1;
-
-
-}
-/**********************************************/
-void finalizeFAST()
-{
-	freeMem(_msf_seqHits, (_msf_seqListSize) * sizeof(int));
-	freeMem(_msf_refGenName, 4*SEQ_LENGTH);
-
-	
-	/*
-	  int i;
-	  for (i=0; i<_msf_rIndexSize; i++)
-	{
-		freeMem(_msf_rIndex[i].seqInfo, _msf_rIndex[i].seqInfo[0]+1);
-	}
-	freeMem(_msf_rIndex, _msf_rIndexSize);*/
-
-
-	freeMem(_msf_map_sort_seqList, sizeof(Pair) * _msf_seqListSize);
-	freeMem(_msf_sort_seqList, sizeof(int) * _msf_seqListSize);
-
-}
-
-/*
-        Will apply the Levenshtein Dynamic programming.
-        Different from verifySingleEndEditDistance fucntion
-	as in this fucntion only one dynamic table is made while
-	in verifySingleEndEditDistance two dynamic table is made
-	for each right and left string
-*/
-int editDistance(int refIndex, char *seq, int seqLength, char *matrix)
-{
-	int i = 0;
-	int size = 0;
-	int error = 0;
-	int rIndex = 0;
-        int directionIndex = 0;
-
-	int min = 0;
-	int minIndex =0;	
-
-	int tempUp = 0;
-	int tempDown = 0;
-	
-	char *ref;
-
-	int errorString = 0;
-        /*
-                1: Up
-                2: Side
-                3: Diagnoal Match
-                4: Diagnoal Mismatch
-        */
-
-	int upValue;
-	int diagValue;
-	int sideValue;
-
-	ref = _msf_refGen + refIndex - 1;
-
-	rIndex = 1;
-
-	for(i=0; i <= errThreshold; i++)
-	{
-		score[0][i] = i;
-		score[i][0] = i;
-	}
-
-	while(rIndex <= seqLength +errThreshold)
-	{
-		tempUp   = ((rIndex - errThreshold) > 0 ? ((rIndex > seqLength) ? seqLength - errThreshold :rIndex - errThreshold) : 1 );
-		tempDown =  ((rIndex >= seqLength-errThreshold ) ? seqLength+1  :rIndex + errThreshold + 1);
-		for(i = tempUp ; i < tempDown ; i++) 
-		{
-			errorString = (*(ref+rIndex-1) == *(seq+i-1));
-
-			upValue   = score[i-1][rIndex]+1;
-			diagValue = score[i-1][rIndex-1]+ !errorString;
-			sideValue = score[i][rIndex-1]+1;
-
-			if(i != tempUp &&  i != tempDown-1) 
-				score[i][rIndex] = min3(sideValue, diagValue , upValue);
-			
-			else if(  (i == ((rIndex - errThreshold) > 0 ? rIndex - errThreshold : 1)) && rIndex <= seqLength  )
-				score[i][rIndex] = min(sideValue, diagValue);
-			else if(rIndex > seqLength &&  (i == seqLength - errThreshold) )
-				 score[i][rIndex] = sideValue;
-			else 
-				score[i][rIndex] = min(diagValue , upValue);
-
-			if(i == tempUp)
-				error = score[i][rIndex];
-			else if(error > score[i][rIndex])
-                                error = score[i][rIndex];
-		}
-		rIndex++;
-	}
-
-	min  = score[seqLength][seqLength+errThreshold];
-	minIndex = seqLength + errThreshold;
-
-	// Find the Best error for all the possible ways.
-	for(i = 1; i <= 2*errThreshold; i++) 
-	{
-		if(min >= score[seqLength][seqLength+errThreshold-i] && seqLength+errThreshold-i > 0)
-		{
-			min = score[seqLength][seqLength+errThreshold-i];
-			minIndex = seqLength+errThreshold-i;
-		}
-	}	
-
-	error = score[seqLength][minIndex];
-
-	directionIndex = seqLength;
-	rIndex = minIndex;
-	while(directionIndex != 0 || rIndex != 0)
-        {
-
-		if(rIndex == 0)
-		{	
-			if(score[directionIndex][rIndex] - score[directionIndex-1][rIndex] == 1)
-                        {
-                                matrix[size] = *(seq+directionIndex-1);
-                                size++;
-                                matrix[size] = 'I';
-                                directionIndex--;
-                        }	
-		}
-		else if(directionIndex == 0)
-		{
-			if(score[directionIndex][rIndex] - score[directionIndex][rIndex-1] == 1)
-                        {
-                                matrix[size] = *(ref+rIndex-1);
-                                size++;
-                                matrix[size] = 'D';
-                                rIndex--;
-                        }
-		}
-		else if(directionIndex-rIndex == errThreshold)
-		{
-			if(score[directionIndex][rIndex] - score[directionIndex-1][rIndex] == 1)
-			{
-				matrix[size] = *(seq+directionIndex-1);
-                                size++;
-                                matrix[size] = 'I';
-                                directionIndex--;
-			}	
-			else if( score[directionIndex][rIndex] - score[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrix[size] = *(ref+rIndex-1);
-	                        rIndex--;
-	                        directionIndex--;
-			}	
-			else
-			{
-				matrix[size] = 'M';
-	                        rIndex--;
-        	                directionIndex--;
-			}
-			
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-		        if(score[directionIndex][rIndex] - score[directionIndex][rIndex-1] == 1)
-                        {
-				matrix[size] = *(ref+rIndex-1);
-                                size++;
-                                matrix[size] = 'D';
-                                rIndex--;
-                        }
-                        else if( score[directionIndex][rIndex] - score[directionIndex-1][rIndex-1] == 1 )
-                        {
-                                matrix[size] = *(ref+rIndex-1);
-                                rIndex--;
-                                directionIndex--;
-                        }
-                        else
-                        {
-                                matrix[size] = 'M';
-                                rIndex--;
-                                directionIndex--;
-                        }
-		}
-		else
-		{
-			if(score[directionIndex][rIndex] - score[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-                        {
-				matrix[size] = *(seq+directionIndex-1);
-                                size++;
-                                matrix[size] = 'I';
-                                directionIndex--;
-                        }
-			else if(score[directionIndex][rIndex] - score[directionIndex][rIndex-1] == 1 && rIndex != 0)
-                        {
-                                matrix[size] = *(ref+rIndex-1);
-                                size++;
-                                matrix[size] = 'D';
-                                rIndex--;
-                        }
-                        else if( score[directionIndex][rIndex] - score[directionIndex-1][rIndex-1] == 1 )
-                        {
-                                matrix[size] = *(ref+rIndex-1);
-                                rIndex--;
-                                directionIndex--;
-                        }
-                        else
-                        {
-                                matrix[size] = 'M';
-                                rIndex--;
-                                directionIndex--;
-                        }
-		}
-                size++;
-        }
-
-        matrix[size] = '\0';
-	
-	char returnString[200];
-	
-	returnString[0] = '\0';
-	reverse(matrix, returnString, size);	
-	sprintf(matrix, "%s", returnString);	
-
-	return error;
-}
-
-/*
-	Will apply the Levenshtein Dynamic programming.
-	in both right and left direction as long as the 
-	threshould error is reached or end of string length
-
-*/
-int msfHashVal(char *seq)
-{
-        int i=0; 
-        int val=0, numericVal=0;
-
-        while(i<6)
-        {
-                switch (seq[i])
-                {
-                        case 'A':
-                                numericVal = 0;
-                                break;
-                        case 'C':
-                                numericVal = 1;
-                                break;
-                        case 'G' :
-                                numericVal = 2;
-                                break;
-                        case 'T':
-                                numericVal = 3;
-                                break;
-                        default:
-                                return -1;
-                                break;
-                }
-                val = (val << 2)|numericVal;
-                i++;
-        }
-        return val;
-}
-
-
-
-int verifySingleEndEditDistance2(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, char *matrix, int *map_location,  short *seqHashValue)
-{
-	int i = 0;
-
-	char *  ref;
-	char *  tempref;
-	
-	int rIndex = 0;				//reference Index
-
-	int e = errThreshold;
-	int error        = 0;
-	int error1       = 0;
-	int totalError   = 0;
-	
-
-	/*
-		1: Up
-		2: Side
-		3: Diagnoal Match
-		4: Diagnoal Mismatch
-	*/
-
-	
-	int minIndex1 = 0;
-	int minIndex2 = 0;
-
-
-	int directionIndex = 0;
-	
-	int size = 0;
-
-	int startIndex1 = 0;
-
-	rIndex = 1;
-
-	
-	char matrixR[200];
-	char matrixL[200];
-	
-	ref = _msf_refGen + refIndex - 1;
-	tempref = _msf_refGen + refIndex - 1;
-
-	int jumpIndex = 0;
-	
-	if(rSeqLength != 0)
-	{
-		error1 = forwardEditDistance2SSE2(ref+segLength+jumpIndex, rSeqLength-jumpIndex, rSeq+jumpIndex, rSeqLength-jumpIndex);
-		if(error1 == -1)
-			return -1;
-	}
-
-
-	if(lSeqLength != 0)
-	{
-		error = backwardEditDistance2SSE2(ref-1, lSeqLength, lSeq+lSeqLength-1, lSeqLength);
-		if(error == -1)
-		{
-			return -1;
-		}
-	}
-
-	matrixL[0] = '\0';
-	matrixR[0] = '\0';
-	
-
-	ref = _msf_refGen + refIndex - 1;
-
-	if(error1+error > errThreshold)
-		return -1;
-
-	ref = _msf_refGen + refIndex - 1;
-	
-	rIndex = startIndex1+1;
-    
-	int i0 = 0;
-	int i1 = 0;
-	int i2 = 0;
-
-	__m128i R0;
-	__m128i R1;
-
-	__m128i Side1, Side2,Side;                    //side matrix
-	__m128i Down1, Down2,Down;                    //down matrix
-	__m128i Diag;                   //
-
-	__m128i tmp;
-
-	/* initialize */
-	R0 = _mm_setzero_si128 ();
-	R1 = _mm_setzero_si128 ();
-	Diag = _mm_setzero_si128 ();
-	Side1 = _mm_setzero_si128 ();
-	Side2 = _mm_setzero_si128 ();
-	Down1 = _mm_setzero_si128 ();
-	Down2 = _mm_setzero_si128 ();
-        Down = _mm_setzero_si128 ();
-        Side = _mm_setzero_si128 ();
-	tmp = _mm_setzero_si128 ();
-	/* end initialize */
-
-	int mismatch[3] = {0,0,0};
-
-	if(lSeqLength != 0)
-	{
-		char *a;
-		char *b;
-
-		a = ref-1;
-		b = lSeq+lSeqLength-1;
-
-		R0 = _mm_insert_epi16(R0,0,0);
-	
-		score[0][0] = 0;
-
-		R1 = _mm_insert_epi16(R1,1,0);
-		R1 = _mm_insert_epi16(R1,1,1);
-		
-		score[1][0] = 1;
-		direction1[1][0] = 1;
-		score[0][1] = 1;		
-		direction1[0][1] = 2;
-		
-		mismatch[0] = ((a[0]) != (b[0]));
-
-		Diag = _mm_insert_epi16(Diag,2*e,0);
-		Diag = _mm_insert_epi16(Diag,mismatch[0],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-
-		Side1 = _mm_insert_epi16(Side1,1,0);
-		Side1 = _mm_insert_epi16(Side1,1,1);
-		Side1 = _mm_insert_epi16(Side1,2*e,2);
-
-		Side2 = _mm_insert_epi16(Side2,2*e,0);
-		Side2 = _mm_insert_epi16(Side2,1,1);
-		Side2 = _mm_insert_epi16(Side2,1,2);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_insert_epi16(Down1,1,1);
-		Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-		Down2 = _mm_insert_epi16(Down2,2*e,0);
-		Down2 = _mm_insert_epi16(Down2,1,1);
-		Down2 = _mm_insert_epi16(Down2,1,2);
-
-		tmp = _mm_slli_si128(R1,2);
-
-		R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-		R0 = _mm_min_epi16(R0,tmp+Down2);
-
-		i0 = _mm_extract_epi16(R0, 0);
-		i1 = _mm_extract_epi16(R0, 1);
-		i2 = _mm_extract_epi16(R0, 2);
-
-		score[0][2] = i0;
-		score[1][1] = i1;
-		score[2][0] = i2; 
-
-		direction1[0][2] = 2;
-		direction1[1][1] = ((mismatch[0] == 0)? 3 : 4);
-		direction1[2][0] = 1; 
-
-		for (i = 3; i  < 2*lSeqLength; i++)
-		{
-			if(i % 2 ==1)
-			{
-				Diag = _mm_sub_epi8(Diag, Diag);
-				mismatch[0] = ( *(a-((i+1)/2-1)) != *(b-((i-1)/2-1)) );
-				Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-				mismatch[1] = ( *(a-((i-1)/2-1)) != *(b-((i+1)/2-1)) );
-				Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-
-				tmp = _mm_srli_si128(R0,2);
-
-				R1 = _mm_min_epi16(tmp+Side1, R1+Diag);
-				R1 = _mm_min_epi16(R1,R0+Down1);
-
-				i0 = _mm_extract_epi16(R1, 0);
-				i1 = _mm_extract_epi16(R1, 1);
-
-				score[i/2][i/2+1] = i0;
-				score[i/2+1][i/2] = i1;
-
-				direction1[i/2][i/2+1] = (score[i/2][i/2+1]==score[i/2-1][i/2] && mismatch[0] == 0)  ? 3 :
-							 (score[i/2][i/2+1]-score[i/2-1][i/2+1]==1)? 1 :
-							 (score[i/2][i/2+1]-score[i/2][i/2]==1)    ? 2 : 4;
-
-				direction1[i/2+1][i/2] = (score[i/2+1][i/2]==score[i/2][i/2-1] && mismatch[1] == 0)  ? 3 :
-                                                         (score[i/2+1][i/2]-score[i/2][i/2]==1)    ? 1 :
-                                                         (score[i/2+1][i/2]-score[i/2+1][i/2-1]==1)? 2 : 4;	
-
-				if(i > 2 * lSeqLength - 2) 
-				{
-					error = min(error, i1);	
-					if(error == i1)
-						minIndex1 = i-lSeqLength;
-				}
-			}
-
-			else if(i % 2 == 0)
-			{
-				mismatch[0] = ( *(a-(i/2))   != *(b-(i/2-2)) );
-				Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-				mismatch[1] = ( *(a-(i/2-1)) != *(b-(i/2-1)) );
-				Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-				mismatch[2] = ( *(a-(i/2-2)) != *(b-(i/2))   );
-				Diag = _mm_insert_epi16(Diag,mismatch[2],2);
-
-				tmp = _mm_slli_si128(R1,2);
-
-				R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-				R0 = _mm_min_epi16(R0,tmp+Down2);
-
-				i0 = _mm_extract_epi16(R0, 0);
-				i1 = _mm_extract_epi16(R0, 1);
-				i2 = _mm_extract_epi16(R0, 2);
-
-				score[i/2-1][i/2+1] = i0;
-				score[i/2][i/2] = i1;
-				score[i/2+1][i/2-1] = i2;
-
-				direction1[i/2-1][i/2+1] = (score[i/2-1][i/2+1]==score[i/2-2][i/2] && mismatch[0] == 0)  ? 3 : (score[i/2-1][i/2+1]-score[i/2-1][i/2]==1)  ? 2 : 4;
-
-                                direction1[i/2][i/2] =   (score[i/2][i/2]==score[i/2-1][i/2-1] && mismatch[1] == 0)  ? 3 :
-                                                         (score[i/2][i/2]-score[i/2-1][i/2]==1)    ? 1 :
-                                                         (score[i/2][i/2]-score[i/2][i/2-1]==1)    ? 2 : 4;
-
-				direction1[i/2+1][i/2-1] =  (score[i/2+1][i/2-1]==score[i/2][i/2-2] && mismatch[2] == 0)  ? 3 :
-                                                            (score[i/2+1][i/2-1]-score[i/2][i/2-1]==1) ? 1 : 4;
-
-				if( (i/2) % segLength == 0 && i1 == 0)	// the segment has been processed no need to process it again
-				{
-					return -1;
-				}
-						
-				if(i == 2 * lSeqLength - 2) 
-				{
-					error = i2;
-					minIndex1 = i-lSeqLength;
-				}
-			}
-		}
-
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		//fill the first part of the error
-		mismatch[0] = ( *(a-(i/2))   != *(b-(i/2-2)) );
-		Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-		mismatch[1] = ( *(a-(i/2-1)) !=*(b-(i/2-1)) );
-		Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-
-		R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-		R0 = _mm_min_epi16(R0,_mm_slli_si128(R1,2)+Down1);
-
-		i0 = _mm_extract_epi16(R0, 0);
-		i1 = _mm_extract_epi16(R0, 1);
-
-		error = min(error, i1);
-		if(error == i1)
-			minIndex1 = i-lSeqLength;
-
-		score[i/2-1][i/2+1] = i0;
-                score[i/2][i/2] = i1;
-
-                direction1[i/2-1][i/2+1] = (score[i/2-1][i/2+1]==score[i/2-2][i/2] && mismatch[0] == 0)  ? 3 :                                        
-                                           (score[i/2-1][i/2+1]-score[i/2-1][i/2])  ? 2 : 4;
-
-                direction1[i/2][i/2] = (score[i/2][i/2]==score[i/2-1][i/2-1] && mismatch[1] == 0)  ? 3 :
-                                       (score[i/2][i/2]-score[i/2-1][i/2]==1)    ? 1 :
-                                       (score[i/2][i/2]-score[i/2][i/2-1]==1)? 2 : 4;
-
-		//fill the second part of the error
-		i++;
-		Diag = _mm_sub_epi8(Diag, Diag);
-		Diag = _mm_insert_epi16(Diag,2*e,0);
-		mismatch[0] = ( *(a-(i/2)) != *(b-(lSeqLength-1)) );
-		Diag = _mm_insert_epi16(Diag,mismatch[0],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-
-		R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-		R1 = _mm_min_epi16(R1,_mm_slli_si128(R0,2)+Down1);
-
-		i0 = _mm_extract_epi16(R1, 0);
-		i1 = _mm_extract_epi16(R1, 1);
-
-		error = min(error, i1);
-		if(error == i1)
-			minIndex1 = i-lSeqLength;
-
-		score[i/2-1][i/2+2] = i0;
-		score[i/2][i/2+1] = i1;
-
-                direction1[i/2-1][i/2+2] = (score[i/2-1][i/2+2]==score[i/2-2][i/2+1] && mismatch[0] == 0)  ? 3 :                     
-                                           (score[i/2-1][i/2+2]-score[i/2-1][i/2+1]==1)    ? 2 : 4;
-
-                direction1[i/2][i/2+1] = (score[i/2][i/2+1]==score[i/2-1][i/2])  ? 3 :
-                                         (score[i/2][i/2+1]-score[i/2-1][i/2+1]==1)? 1 :
-                                         (score[i/2][i/2+1]-score[i/2][i/2]==1)? 2 : 4;
-
-		//fill the last the last element of the matrix
-		i++;
-		Diag = _mm_sub_epi8(Diag, Diag);
-		mismatch[0] = ( *(a-(i/2)) != *(b-(lSeqLength-1)) );
-		Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-
-		Down = _mm_insert_epi16(Down,1,0);
-
-		Side = _mm_insert_epi16(Side,1,0);
-
-		tmp = _mm_srli_si128(R1,2);
-
-		R0 = _mm_min_epi16(R1+Down, R0+Diag);
-		R0 = _mm_min_epi16(R0,tmp+Side);
-
-		i0 = _mm_extract_epi16(R0, 0);
-
-		error = min(error, i0);
-		if(error == 0)
-			return -1;
-		if(error == i0)
-			minIndex1 = i-lSeqLength;
-		if(mismatch[0] == 0)
-			direction1[lSeqLength][lSeqLength+errThreshold] = 3;
-		else	
-		{
-			if(score[lSeqLength][lSeqLength+errThreshold] - score[lSeqLength][lSeqLength+errThreshold-1] == 1)
-				direction1[lSeqLength][lSeqLength+errThreshold] = 2;
-			else if(score[lSeqLength][lSeqLength+errThreshold] - score[lSeqLength-1][lSeqLength+errThreshold] == 1)
-				direction1[lSeqLength][lSeqLength+errThreshold] = 1;
-			else
-				direction1[lSeqLength][lSeqLength+errThreshold] = 4;
-		}		
-	}
-	error1   = error;
-	error    = 0;
-
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-
-	
-	*map_location = ((lSeqLength == 0) ? refIndex : refIndex - rIndex) ;
-
-	ref = ref + segLength;
- 
-	if(rSeqLength <= e)
-	{
-		char *a;
-		char *b;
-		
-		int tmp_index = 0;
-		
-		a = ref;
-		b = rSeq;
-		
-		for(tmp_index = 0; tmp_index < rSeqLength; tmp_index++)
-		{
-			matrixR[tmp_index] = (a[tmp_index]==b[tmp_index]) ? 'M' : a[tmp_index]  ;
-		}
-		matrixR[tmp_index] = '\0';
-	}
-	else if(rSeqLength != 0 && rSeqLength >= e)
-	{
-		char *a;
-		char *b;
-
-		a = ref;
-		b = rSeq;
-
-		R0 = _mm_sub_epi8(R0, R0);
-		R1 = _mm_sub_epi8(R1, R1);
-
-		R0 = _mm_insert_epi16(R0,0,0);
-	
-		score[0][0] = 0;
-
-		R1 = _mm_insert_epi16(R1,1,0);
-		R1 = _mm_insert_epi16(R1,1,1);
-		
-		score[1][0] = 1;
-		direction2[1][0] = 1;
-		score[0][1] = 1;		
-		direction2[0][1] = 2;
-		
-		mismatch[0] = ((a[0]) != (b[0]));
-
-		Diag = _mm_insert_epi16(Diag,2*e,0);
-		Diag = _mm_insert_epi16(Diag,mismatch[0],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-
-		Side1 = _mm_insert_epi16(Side1,1,0);
-		Side1 = _mm_insert_epi16(Side1,1,1);
-		Side1 = _mm_insert_epi16(Side1,2*e,2);
-
-		Side2 = _mm_insert_epi16(Side2,2*e,0);
-		Side2 = _mm_insert_epi16(Side2,1,1);
-		Side2 = _mm_insert_epi16(Side2,1,2);
-
-		Down1 = _mm_insert_epi16(Down1,1,0);
-		Down1 = _mm_insert_epi16(Down1,1,1);
-		Down1 = _mm_insert_epi16(Down1,2*e,2);
-
-		Down2 = _mm_insert_epi16(Down2,2*e,0);
-		Down2 = _mm_insert_epi16(Down2,1,1);
-		Down2 = _mm_insert_epi16(Down2,1,2);
-
-		tmp = _mm_slli_si128(R1,2);
-
-		R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-		R0 = _mm_min_epi16(R0,tmp+Down2);
-
-		i0 = _mm_extract_epi16(R0, 0);
-		i1 = _mm_extract_epi16(R0, 1);
-		i2 = _mm_extract_epi16(R0, 2);
-
-		score[0][2] = i0;
-		score[1][1] = i1;
-		score[2][0] = i2; 
-
-		direction2[0][2] = 2;
-		direction2[1][1] = ((mismatch[0] == 0)? 3 : 4);
-		direction2[2][0] = 1; 
-
-
-		for (i = 3; i  < 2*rSeqLength; i++)
-		{
-			if(i % 2 ==1)
-			{
-				Diag = _mm_sub_epi8(Diag, Diag);
-				mismatch[0] = ((a[(i+1)/2-1]) != (b[(i-1)/2-1]));
-				Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-				mismatch[1] = ((a[(i-1)/2-1]) != (b[(i+1)/2-1]));
-				Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-
-				tmp = _mm_srli_si128(R0,2);
-
-				R1 = _mm_min_epi16(tmp+Side1, R1+Diag);
-				R1 = _mm_min_epi16(R1,R0+Down1);
-
-				i0 = _mm_extract_epi16(R1, 0);
-				i1 = _mm_extract_epi16(R1, 1);
-
-				score[i/2][i/2+1] = i0;
-				score[i/2+1][i/2] = i1;
-
-				direction2[i/2][i/2+1] = (score[i/2][i/2+1]==score[i/2-1][i/2] && mismatch[0] == 0)  ? 3 :
-										 (score[i/2][i/2+1]-score[i/2-1][i/2+1]==1)? 1 :
-										 (score[i/2][i/2+1]-score[i/2][i/2]==1)    ? 2 : 4;
-
-				direction2[i/2+1][i/2] = (score[i/2+1][i/2]==score[i/2][i/2-1] && mismatch[1] == 0)  ? 3 :
-										 (score[i/2+1][i/2]-score[i/2][i/2]==1)    ? 1 :
-										 (score[i/2+1][i/2]-score[i/2+1][i/2-1]==1)? 2 : 4;
-
-
-				if(i > 2 * rSeqLength - 2) 
-				{
-					error = min(error, i1);	
-					if(error == i1)
-						minIndex2 = i-rSeqLength;
-				}
-			}
-
-			else if(i % 2 == 0)
-			{
-				mismatch[0] = ((a[i/2]) != (b[i/2-2]));
-				Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-				mismatch[1] = ((a[i/2-1]) != (b[i/2-1]));
-				Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-				mismatch[2] = ((a[i/2-2]) != (b[i/2]));
-				Diag = _mm_insert_epi16(Diag,mismatch[2],2);
-
-				tmp = _mm_slli_si128(R1,2);
-
-				R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-				R0 = _mm_min_epi16(R0,tmp+Down2);
-
-				i0 = _mm_extract_epi16(R0, 0);
-				i1 = _mm_extract_epi16(R0, 1);
-				i2 = _mm_extract_epi16(R0, 2);
-
-				score[i/2-1][i/2+1] = i0;
-				score[i/2][i/2] = i1;
-				score[i/2+1][i/2-1] = i2;
-
-				direction2[i/2-1][i/2+1] = (score[i/2-1][i/2+1]==score[i/2-2][i/2] && mismatch[0] == 0)  ? 3 :
-										   (score[i/2-1][i/2+1]-score[i/2-1][i/2]==1)  ? 2 : 4;
-
-				direction2[i/2][i/2] =   (score[i/2][i/2]==score[i/2-1][i/2-1] && mismatch[1] == 0)  ? 3 :
-										 (score[i/2][i/2]-score[i/2-1][i/2]==1)    ? 1 :
-										 (score[i/2][i/2]-score[i/2][i/2-1]==1)    ? 2 : 4;
-
-				direction2[i/2+1][i/2-1] =  (score[i/2+1][i/2-1]==score[i/2][i/2-2] && mismatch[2]==0)  ? 3 :
-											(score[i/2+1][i/2-1]-score[i/2][i/2-1]==1) ? 1 : 4;	
-
-				
-				if(i == 2 * rSeqLength - 2) 
-				{
-					error = i2;
-					minIndex2 = i-rSeqLength;
-				}
-			}
-		}
-
-		Down1 = _mm_insert_epi16(Down1,2*e,0);
-
-		//fill the first part of the error
-		mismatch[0] = ((a[i/2]) != (b[i/2-2]));
-		Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-		mismatch[1] = ((a[i/2-1]) != (b[i/2-1]));
-		Diag = _mm_insert_epi16(Diag,mismatch[1],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-
-		R0 = _mm_min_epi16(R1+Side1, R0+Diag);
-		R0 = _mm_min_epi16(R0,_mm_slli_si128(R1,2)+Down1);
-
-		i0 = _mm_extract_epi16(R0, 0);
-		i1 = _mm_extract_epi16(R0, 1);
-
-		error = min(error, i1);
-		if(error == i1)
-			minIndex2 = i-rSeqLength;
-
-		score[i/2-1][i/2+1] = i0;
-		score[i/2][i/2] = i1;
-
-                direction2[i/2-1][i/2+1] = (score[i/2-1][i/2+1]==score[i/2-2][i/2] && mismatch[0] == 0)  ? 3 : 
-										   (score[i/2-1][i/2+1]-score[i/2-1][i/2]==1)    ? 2 : 4;
-
-                direction2[i/2][i/2] = (score[i/2][i/2]==score[i/2-1][i/2-1] && mismatch[1] == 0)  ? 3 :
-                                       (score[i/2][i/2]-score[i/2-1][i/2]==1)    ? 1 :
-                                       (score[i/2][i/2]-score[i/2][i/2-1]==1)? 2 : 4;
-
-
-		//fill the second part of the error
-		i++;
-		Diag = _mm_sub_epi8(Diag, Diag);
-		Diag = _mm_insert_epi16(Diag,2*e,0);
-		mismatch[0] = ((a[i/2]) != (b[rSeqLength-1]));
-		Diag = _mm_insert_epi16(Diag,mismatch[0],1);
-		Diag = _mm_insert_epi16(Diag,2*e,2);
-		
-		R1 = _mm_min_epi16(R0+Side1, _mm_slli_si128(R1,2)+Diag);
-		R1 = _mm_min_epi16(R1,_mm_slli_si128(R0,2)+Down1);
-
-		i0 = _mm_extract_epi16(R1, 0);
-		i1 = _mm_extract_epi16(R1, 1);
-
-		error = min(error, i1);
-		if(error == i1)
-			minIndex2 = i-rSeqLength;
-
-		score[i/2-1][i/2+2] = i0;
-		score[i/2][i/2+1] = i1;
-
-                direction2[i/2-1][i/2+2] = (score[i/2-1][i/2+2]==score[i/2-2][i/2+1] && mismatch[0] == 0)  ? 3 :
-                                           (score[i/2-1][i/2+2]-score[i/2-1][i/2+1]==1)  ? 2 : 3;
-
-                direction2[i/2][i/2+1] = (score[i/2][i/2+1]==score[i/2-1][i/2] && mismatch[0] == 0)  ? 3 :
-                                         (score[i/2][i/2+1]-score[i/2-1][i/2+1]==1)? 1 :
-                                         (score[i/2][i/2+1]-score[i/2][i/2]==1)? 2 : 4;
-
-
-		//fill the last the last element of the matrix
-		i++;
-		Diag = _mm_sub_epi8(Diag, Diag);
-		mismatch[0] = ((a[i/2]) != (b[rSeqLength-1]));
-		Diag = _mm_insert_epi16(Diag,mismatch[0],0);
-
-		Down = _mm_sub_epi8(Down, Down);
-		Down = _mm_insert_epi16(Down,1,0);
-
-		Side = _mm_sub_epi8(Side, Side);
-		Side = _mm_insert_epi16(Side,1,0);
-
-		tmp = _mm_srli_si128(R1,2);
-
-		R0 = _mm_min_epi16(R1+Down, R0+Diag);
-		R0 = _mm_min_epi16(R0,tmp+Side);
-
-		i0 = _mm_extract_epi16(R0, 0);
-
-		error = min(error, i0);
-		if(error == i0)
-			minIndex2 = i-rSeqLength;
-
-		if(mismatch[0] == 0)
-			direction2[rSeqLength][rSeqLength+errThreshold] = 3;
-		else
-		{
-			if(score[rSeqLength][rSeqLength+errThreshold] - score[rSeqLength][rSeqLength+errThreshold-1] == 1)
-				direction2[lSeqLength][lSeqLength+errThreshold] = 2;
-			else if(score[rSeqLength][rSeqLength+errThreshold] - score[rSeqLength-1][rSeqLength+errThreshold] == 1)
-				direction2[rSeqLength][rSeqLength+errThreshold] = 1;
-			else
-				direction2[rSeqLength][rSeqLength+errThreshold] = 4;
-		}
-
-	}
-
-	totalError = error1 + error;
-
-	size = 0;
-	directionIndex = rSeqLength;
-	rIndex = minIndex2;
-
-
-	if(rSeqLength > e)
-	{
-		while(directionIndex != 0 || rIndex != 0)
-		{
-
-			if(direction2[directionIndex][rIndex] == 3)
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-			else if(direction2[directionIndex][rIndex] == 4)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else if(direction2[directionIndex][rIndex] == 2)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}
-			size++;
-		}
-		matrixR[size] = '\0';
-	}
-	size = 0;
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-	
-	while(directionIndex != 0 || rIndex != 0)
-	{
-
-		if(direction1[directionIndex][rIndex] == 3)
-		{
-			matrixL[size] = 'M';
-			rIndex--;
-			directionIndex--;
-		}
-		else if(direction1[directionIndex][rIndex] == 4)
-		{
-			matrixL[size] = *(tempref-rIndex);
-			rIndex--;
-			directionIndex--;
-		}
-		else if(direction1[directionIndex][rIndex] == 2)
-		{
-			matrixL[size] = 'D';                    
-			size++;
-			matrixL[size] = *(tempref-rIndex);
-			rIndex--;                 
-		}
-		else
-		{
-			matrixL[size] = 'I';
-			size++;
-			matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-			directionIndex--;                      
-		}
-
-		size++;
-	}
-
-	matrixL[size] = '\0';
-	
-	char middle[200];
-	middle[0] = '\0';
-	
-	for(i = 0; i < segLength; i++)
-		middle[i] = 'M';
-	middle[segLength] = '\0';
-
-	char rmatrixR[200];
-
-	reverse(matrixR, rmatrixR, strlen(matrixR));
-
-	sprintf(matrix, "%s%s%s", matrixL, middle, rmatrixR);
-
-	return totalError;
-}
-
-int verifySingleEndEditDistance4(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, char *matrix, int *map_location,  short *seqHashValue)
-{
-
-	int i = 0;
-	
-	char *  ref;
-	char *  tempref;
-	
-	int rIndex = 0;				//reference Index
-
-	int error        = 0;
-	int error1       = 0;
-
-	int error2   	 = 0;
-	int error3 	 = 0;
-	int totalError   = 0;
-	int errorSegment = 0;
-
-	int ERROR_BOUND = errThreshold;
-
-	
-	/*
-		1: Up
-		2: Side
-		3: Diagnoal Match
-		4: Diagnoal Mismatch
-	*/
-
-	int min = 0;
-	int minIndex1 = 0;
-	int minIndex2 = 0;
-
-	int directionIndex = 0;
-	
-	
-	int size = 0;
-
-	ref = _msf_refGen + refIndex - 1;
-	tempref = _msf_refGen + refIndex - 1;
-
-
-	if(lSeqLength != 0)
-	{
-		error3 = backwardEditDistance4SSE2(ref-1, lSeqLength, lSeq+lSeqLength-1, lSeqLength);
-		if(error3 == -1 || error3 == 0){
-			return -1;
-		}
-	}
-
-	if(rSeqLength != 0)
-	{
-		error2 = forwardEditDistance4SSE2(ref+segLength, rSeqLength, rSeq, rSeqLength);
-		if(error2 == -1)
-			return -1;
-	}
-
-	if(error2 + error3 > errThreshold)
-		return -1;
-
-	rIndex = 1;
-
-	int prevError = 0;
-
-	int tempUp = 0;
-	int tempDown = 0;
-
-	int errorString = 0;
-		
-	int upValue;
-	int diagValue;
-	int sideValue;
-	
-	while(rIndex <= lSeqLength+errThreshold  && lSeqLength != 0)
-	{
-		tempUp   = ((rIndex - ERROR_BOUND) > 0 ? ((rIndex > lSeqLength) ? lSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1 );
-		tempDown =  ((rIndex >= lSeqLength-ERROR_BOUND ) ? lSeqLength+1  :rIndex + ERROR_BOUND + 1);
-		for(i = tempUp ; i < tempDown ; i++) 
-		{
-			errorString = (*(ref-rIndex) == *(lSeq+lSeqLength-i));
-
-			upValue   = scoreB[i-1][rIndex]+1;
-			diagValue = scoreB[i-1][rIndex-1]+ !errorString;
-			sideValue = scoreB[i][rIndex-1]+1;
-
-			if(i != tempUp &&  i != tempDown-1) 
-				scoreB[i][rIndex] = min3(sideValue, diagValue , upValue);
-			
-			else if(  (i == ((rIndex - ERROR_BOUND) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= lSeqLength  )
-				scoreB[i][rIndex] = min(sideValue, diagValue);
-			else if(rIndex > lSeqLength &&  (i == lSeqLength - ERROR_BOUND) )
-				 scoreB[i][rIndex] = sideValue;
-			else 
-				scoreB[i][rIndex] = min(diagValue , upValue);
-
-			if(i == tempUp)
-				error = scoreB[i][rIndex];
-			else if(error > scoreB[i][rIndex])
-                                error = scoreB[i][rIndex];
-		}
-		if(rIndex <= lSeqLength)
-		{
-			errorSegment = error-prevError;
-		}
-		rIndex++;
-	}
-
-	if(lSeqLength != 0)
-	{
-		min  = scoreB[lSeqLength][lSeqLength+errThreshold];
-		minIndex1 = lSeqLength + errThreshold;
-
-		// Find the Best error for all the possible ways.
-		for(i = 1; i <= 2*errThreshold; i++) 
-		{
-			if(min >= scoreB[lSeqLength][lSeqLength+errThreshold-i] && lSeqLength+errThreshold-i > 0)
-			{
-				min = scoreB[lSeqLength][lSeqLength+errThreshold-i];
-				minIndex1 = lSeqLength+errThreshold-i;
-			}
-		}	
-		error = scoreB[lSeqLength][minIndex1];
-	}
-	
-	error1   = error;
-
-	error    = 0;
-	errorSegment = 0;
-
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-	
-
-	*map_location = ((lSeqLength == 0) ? refIndex : refIndex - rIndex) ;
-
-	ref = ref + segLength;
-
-	if(rSeqLength != 0)
-	{
-		rIndex = 1;
-		while(rIndex <= rSeqLength+errThreshold-error1)
-		{
-			tempUp   = (rIndex - ERROR_BOUND) > 0 ? ((rIndex > rSeqLength) ? rSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1;
-			tempDown = ((rIndex >= rSeqLength- ERROR_BOUND ) ? rSeqLength+1  :rIndex + ERROR_BOUND + 1);
-			for(i = tempUp; i < tempDown ; i++)
-			{
-				errorString = (*(ref+rIndex-1) == *(rSeq+i-1));
-
-				upValue   = scoreF[i-1][rIndex]+1;
-				diagValue = scoreF[i-1][rIndex-1]+ !errorString;
-				sideValue = scoreF[i][rIndex-1]+1;
-
-				if(i != tempUp &&  i != tempDown-1)
-					scoreF[i][rIndex] = min3(sideValue, diagValue , upValue);
-				else if(  (i == ((rIndex - ERROR_BOUND ) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= rSeqLength  )
-					scoreF[i][rIndex] = min(sideValue, diagValue);
-				else if(rIndex > rSeqLength &&  (i == rSeqLength - ERROR_BOUND) )
-					scoreF[i][rIndex] = sideValue;	                    
-				else
-					scoreF[i][rIndex] = min(diagValue , upValue);
-
-				if(i == tempUp)
-					error = scoreF[i][rIndex];
-				if(error > scoreF[i][rIndex])
-					error = scoreF[i][rIndex];
-			}
-			if(rIndex <= rSeqLength)
-			{
-				errorSegment = error;
-			}
-
-			rIndex++;
-		}
-
-		min  = scoreF[rSeqLength][rSeqLength+errThreshold-error1];
-		minIndex2 = rSeqLength + errThreshold-error1;
-
-		// Find the Best error for all the possible ways.
-		for(i = 1; i <= 2*(errThreshold-error1); i++)
-		{
-			if(min > scoreF[rSeqLength][rSeqLength+errThreshold-error1-i] && rSeqLength+errThreshold-error1-i > 0)
-			{
-				min = scoreF[rSeqLength][rSeqLength+errThreshold-error1-i];
-				minIndex2 = rSeqLength+errThreshold-error1-i;
-			}
-		}
-		error = scoreF[rSeqLength][minIndex2];
-	}
-
-	totalError = error + error1;
-
-	if(errThreshold > 4)
-		printf("ERROR in errorThreshold.\n");
-
-
-	if(totalError != error2 + error3 && totalError > errThreshold)
-	{
-		printf("ErrorF=%d, ErrorB=%d Error=%d Error=%d\n", error2,error3,error1,error);
-
-		scanf("%d", &i);
-	}
-
-	char matrixR[200];
-	char matrixL[200];
-
-	matrixR[0] = '\0';
-	matrixL[0] = '\0';
-
-	size = 0;
-	directionIndex = rSeqLength;
-	rIndex = minIndex2;
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}	
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}	
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}
-			else if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		size++;
-	}
-	matrixR[size] = '\0';	
-        
-	size = 0;
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-
-		size++;
-	}
-	
-	matrixL[size] = '\0';
-	char middle[200];
-	middle[0] = '\0';
-	
-	for(i = 0; i < segLength; i++)
-		middle[i] = 'M';
-	middle[segLength] = '\0';
-
-	char rmatrixR[200];
-
-	reverse(matrixR, rmatrixR, strlen(matrixR));
-
-	sprintf(matrix, "%s%s%s", matrixL, middle, rmatrixR);
-
-	return totalError;
-
-}
-
-int verifySingleEndEditDistanceExtention(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, 
-					char *matrix, int *map_location, short *seqHashValue)
-{
-	int i = 0;
-	
-	char *  ref;
-	char *  tempref;
-	
-	int rIndex = 0;				//reference Index
-
-	int error        = 0;
-	int error1       = 0;
-
-	int error2   	 = 0;
-	int error3 	 = 0;
-	int totalError   = 0;
-	int errorSegment = 0;
-
-	int ERROR_BOUND = min(4, errThreshold);
-	
-
-	/*
-		1: Up
-		2: Side
-		3: Diagnoal Match
-		4: Diagnoal Mismatch
-	*/
-
-	int min = 0;
-	int minIndex1 = 0;
-	int minIndex2 = 0;
-
-	int directionIndex = 0;
-	
-	
-	int size = 0;
-
-	ref = _msf_refGen + refIndex - 1;
-	tempref = _msf_refGen + refIndex - 1;
-
-
-	if(lSeqLength != 0)
-	{
-		error3 = backwardEditDistanceSSE2Extention(ref-1, lSeqLength, lSeq+lSeqLength-1, lSeqLength);
-		if(error3 == -1){
-			return -1;
-		}
-	}
-
-	if(rSeqLength != 0)
-	{
-		error2 = forwardEditDistanceSSE2Extention(ref+segLength, rSeqLength, rSeq, rSeqLength);
-		if(error2 == -1)
-			return -1;
-	}
-
-	if(error2 + error3 > errThreshold)
-		return -1;	
-
-	rIndex = 1;
-
-	int prevError = 0;
-
-	int tempUp = 0;
-	int tempDown = 0;
-
-	int errorString = 0;
-		
-	int upValue;
-	int diagValue;
-	int sideValue;
-	if(lSeqLength > ERROR_BOUND)
-	{	
-		while(rIndex <= lSeqLength+ERROR_BOUND  && lSeqLength != 0)
-		{
-			tempUp   = ((rIndex - ERROR_BOUND) > 0 ? ((rIndex > lSeqLength) ? lSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1 );
-			tempDown =  ((rIndex >= lSeqLength-ERROR_BOUND ) ? lSeqLength+1  :rIndex + ERROR_BOUND + 1);
-			for(i = tempUp ; i < tempDown ; i++) 
-			{
-				errorString = (*(ref-rIndex) == *(lSeq+lSeqLength-i));
-
-				upValue   = scoreB[i-1][rIndex]+1;
-				diagValue = scoreB[i-1][rIndex-1]+ !errorString;
-				sideValue = scoreB[i][rIndex-1]+1;
-
-				if(i != tempUp &&  i != tempDown-1) 
-					scoreB[i][rIndex] = min3(sideValue, diagValue , upValue);
-
-				else if(  (i == ((rIndex - ERROR_BOUND) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= lSeqLength  )
-					scoreB[i][rIndex] = min(sideValue, diagValue);
-				else if(rIndex > lSeqLength &&  (i == lSeqLength - ERROR_BOUND) )
-					scoreB[i][rIndex] = sideValue;
-				else 
-					scoreB[i][rIndex] = min(diagValue , upValue);
-
-				if(i == tempUp)
-					error = scoreB[i][rIndex];
-				else if(error > scoreB[i][rIndex])
-					error = scoreB[i][rIndex];
-			}
-			if(rIndex <= lSeqLength)
-			{
-				errorSegment = error-prevError;
-			}
-			rIndex++;
-		}
-
-		if(lSeqLength != 0)
-		{
-			min  = scoreB[lSeqLength][lSeqLength+ERROR_BOUND];
-			minIndex1 = lSeqLength + ERROR_BOUND;
-
-			// Find the Best error for all the possible ways.
-			for(i = 1; i <= 2*ERROR_BOUND; i++) 
-			{
-				if(min >= scoreB[lSeqLength][lSeqLength+ERROR_BOUND-i] && lSeqLength+ERROR_BOUND-i > 0)
-				{
-					min = scoreB[lSeqLength][lSeqLength+ERROR_BOUND-i];
-					minIndex1 = lSeqLength+ERROR_BOUND-i;
-				}
-			}	
-			error = scoreB[lSeqLength][minIndex1];
-		}
-	}
-	else
-	{
-		int j = 0;
-		for(i = 1; i <= lSeqLength; i++)
-		{
-			for(j = 1; j <= lSeqLength; j++)
-			{
-				scoreB[i][j] = min3(scoreB[i-1][j-1]+ (*(ref-j) != *(lSeq+lSeqLength-i) ),scoreB[i][j-1]+1 ,scoreB[i-1][j]+1);
-			}
-		}
-		error = scoreB[lSeqLength][lSeqLength];
-		minIndex1 = lSeqLength;
-
-	}
-	error1   = error;
-
-	error    = 0;
-	errorSegment = 0;
-
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-	
-	*map_location = ((lSeqLength == 0) ? refIndex : refIndex - rIndex) ;
-
-	ref = ref + segLength;
-	
-	if(rSeqLength != 0 && rSeqLength > ERROR_BOUND)
-	{
-		ERROR_BOUND = min(ERROR_BOUND, rSeqLength);
-		
-		if(rSeqLength == ERROR_BOUND)
-		{
-			for(i=0; i < 2*ERROR_BOUND; i++)
-				scoreF[0][i] = i;
-		}
-
-		rIndex = 1;
-		while(rIndex <= rSeqLength+ERROR_BOUND)
-		{
-			tempUp   = (rIndex - ERROR_BOUND) > 0 ? ((rIndex > rSeqLength) ? rSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1;
-			tempDown = ((rIndex >= rSeqLength- ERROR_BOUND ) ? rSeqLength+1  :rIndex + ERROR_BOUND + 1);
-			for(i = tempUp; i < tempDown ; i++)
-			{
-				errorString = (*(ref+rIndex-1) == *(rSeq+i-1));
-				upValue   = scoreF[i-1][rIndex]+1;
-				diagValue = scoreF[i-1][rIndex-1]+ !errorString;
-				sideValue = scoreF[i][rIndex-1]+1;
-
-				if(i != tempUp &&  i != tempDown-1)
-					scoreF[i][rIndex] = min3(sideValue, diagValue , upValue);
-				else if(  (i == ((rIndex - ERROR_BOUND ) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= rSeqLength  )
-					scoreF[i][rIndex] = min(sideValue, diagValue);
-				else if(rIndex > rSeqLength &&  (i == rSeqLength - ERROR_BOUND) )
-					scoreF[i][rIndex] = sideValue;	                    
-				else
-					scoreF[i][rIndex] = min(diagValue , upValue);
-
-				if(i == tempUp)
-					error = scoreF[i][rIndex];
-				if(error > scoreF[i][rIndex])
-					error = scoreF[i][rIndex];
-			}
-			if(rIndex <= rSeqLength)
-			{
-				errorSegment = error;
-			}
-			rIndex++;
-		}
-		min  = scoreF[rSeqLength][rSeqLength+ERROR_BOUND];
-		minIndex2 = rSeqLength + ERROR_BOUND;
-
-		// Find the Best error for all the possible ways.
-		for(i = 1; i <= 2*ERROR_BOUND; i++)
-		{
-			if(min > scoreF[rSeqLength][rSeqLength+ERROR_BOUND-i] && rSeqLength+ERROR_BOUND-i > 0)
-			{
-				min = scoreF[rSeqLength][rSeqLength+ERROR_BOUND-i];
-				minIndex2 = rSeqLength+ERROR_BOUND-i;
-			}
-		}
-		error = scoreF[rSeqLength][minIndex2];
-	}
-	else
-	{
-		int j = 0;
-		for(i = 1; i <= rSeqLength; i++)
-		{
-			for(j = 1; j <= rSeqLength; j++)
-			{
-				scoreF[i][j] = min3(scoreF[i-1][j-1]+ (*(ref+j-1) != *(rSeq+i-1) ),scoreF[i][j-1]+1 ,scoreF[i-1][j]+1);
-			}
-		}
-		error = scoreF[rSeqLength][rSeqLength];
-		minIndex2 = rSeqLength;
-	}
-
-        totalError = error + error1;
-
-	if(totalError  != error2+error3)
-	{
-		for(i = 0; i < lSeqLength; i++)
-			printf("%c", *(tempref-1-i));
-		printf("\n");
-		for(i = 0; i < lSeqLength; i++)
-			printf("%c", *(lSeq+i));
-		printf("\n");
-
-		for(i = 0; i < rSeqLength; i++)
-			printf("%c", *(tempref+segLength+i));
-		printf("\n");
-
-		for(i = 0; i < rSeqLength; i++)
-			printf("%c", *(rSeq+i));
-		printf("\n");
-
-		printf("ERROR=%d\n", totalError);
-		printf("ERROR_SSE=%d\n", error3+error2);
-
-		printf("ERROR_SSE_back=%d E_SSE_forw=%d\n", error3, error2);
-		printf("ERROR_back=%d E_forw=%d\n", error1, error);
-
-	}
-
-	char matrixR[200];
-	char matrixL[200];
-
-	matrixR[0] = '\0';
-	matrixL[0] = '\0';
-
-	size = 0;
-	directionIndex = rSeqLength;
-	rIndex = minIndex2;
-
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}	
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}	
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}
-			else if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		size++;
-	}
-	matrixR[size] = '\0';	
-        
-	size = 0;
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		size++;
-	}
-	matrixL[size] = '\0';
-
-	char middle[200];
-	middle[0] = '\0';
-	for(i = 0; i < segLength; i++)
-		middle[i] = 'M';
-	middle[segLength] = '\0';
-
-	char rmatrixR[200];
-
-	reverse(matrixR, rmatrixR, strlen(matrixR));
-
-	sprintf(matrix, "%s%s%s", matrixL, middle, rmatrixR);
-
-	
-	return totalError;
-
-}
-
-
-int verifySingleEndEditDistance(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, char *matrix, int *map_location, short *seqHashValue)
-{
-
-	int i = 0;
-	
-	char *  ref;
-	char *  tempref;
-	
-	int rIndex = 0;				//reference Index
-
-	int error        = 0;
-	int error1       = 0;
-
-	int error2 	 = 0;
-	int error3	 = 0;
-
-	int totalError   = 0;
-	int errorSegment = 0;
-
-	int ERROR_BOUND = errThreshold;
-
-	/*
-		1: Up
-		2: Side
-		3: Diagnoal Match
-		4: Diagnoal Mismatch
-	*/
-
-	int min = 0;
-	int minIndex1 = 0;
-	int minIndex2 = 0;
-
-	int directionIndex = 0;
-	
-	
-	int size = 0;
-
-	ref = _msf_refGen + refIndex - 1;
-	tempref = _msf_refGen + refIndex - 1;
-
-
-	if(rSeqLength != 0)
-	{
-		if(errThreshold %2 == 1)
-			error2 = forwardEditDistanceSSE2Odd(ref+segLength, rSeqLength, rSeq, rSeqLength);
-		else	
-			error2 = forwardEditDistanceSSE2G(ref+segLength, rSeqLength, rSeq, rSeqLength);
-		if(error2 == -1)
-			return -1;
-	}
-
-	if(lSeqLength != 0)
-	{
-		if(errThreshold % 2 == 1)
-			error3 = backwardEditDistanceSSE2Odd(ref-1, lSeqLength, lSeq+lSeqLength-1, lSeqLength);
-		else
-			error3 = backwardEditDistanceSSE2G(ref-1, lSeqLength, lSeq+lSeqLength-1, lSeqLength);
-		if(error3 == -1 || error3 == 0){
-			return -1;
-		}
-	}
-
-	if(error3 + error2 > errThreshold)
-		return -1;
-
-	for(i = 0 ; i < errThreshold + 1; i++) 
-	{
-		scoreB[0][i] = i;
-		scoreB[i][0] = i;
-	}
-
-	rIndex = 1;
-	int prevError = 0;
-
-	int tempUp = 0;
-	int tempDown = 0;
-
-	int errorString = 0;
-		
-	int upValue;
-	int diagValue;
-	int sideValue;
-	
-	while(rIndex <= lSeqLength+errThreshold  && lSeqLength != 0)
-	{
-		tempUp   = ((rIndex - ERROR_BOUND) > 0 ? ((rIndex > lSeqLength) ? lSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1 );
-		tempDown =  ((rIndex >= lSeqLength-ERROR_BOUND ) ? lSeqLength+1  :rIndex + ERROR_BOUND + 1);
-		for(i = tempUp ; i < tempDown ; i++) 
-		{
-			errorString = (*(ref-rIndex) == *(lSeq+lSeqLength-i));
-
-			upValue   = scoreB[i-1][rIndex]+1;
-			diagValue = scoreB[i-1][rIndex-1]+ !errorString;
-			sideValue = scoreB[i][rIndex-1]+1;
-
-			if(i != tempUp &&  i != tempDown-1) 
-				scoreB[i][rIndex] = min3(sideValue, diagValue , upValue);
-			
-			else if(  (i == ((rIndex - ERROR_BOUND) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= lSeqLength  )
-				scoreB[i][rIndex] = min(sideValue, diagValue);
-			else if(rIndex > lSeqLength &&  (i == lSeqLength - ERROR_BOUND) )
-				 scoreB[i][rIndex] = sideValue;
-			else 
-				scoreB[i][rIndex] = min(diagValue , upValue);
-
-			if(i == tempUp)
-				error = scoreB[i][rIndex];
-			else if(error > scoreB[i][rIndex])
-                                error = scoreB[i][rIndex];
-		}
-		if(rIndex <= lSeqLength)
-		{
-			errorSegment = error-prevError;
-		}
-		rIndex++;
-	}
-	if(lSeqLength != 0)
-	{
-		min  = scoreB[lSeqLength][lSeqLength+errThreshold];
-		minIndex1 = lSeqLength + errThreshold;
-
-		// Find the Best error for all the possible ways.
-		for(i = 1; i <= 2*errThreshold; i++) 
-		{
-			if(min >= scoreB[lSeqLength][lSeqLength+errThreshold-i] && lSeqLength+errThreshold-i > 0)
-			{
-				min = scoreB[lSeqLength][lSeqLength+errThreshold-i];
-				minIndex1 = lSeqLength+errThreshold-i;
-			}
-		}	
-		error = scoreB[lSeqLength][minIndex1];
-	}
-	
-	error1   = error;
-
-	error    = 0;
-	errorSegment = 0;
-
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-	
-	*map_location = ((lSeqLength == 0) ? refIndex : refIndex - rIndex) ;
-
-	ref = ref + segLength;
-
-	if(rSeqLength != 0)
-	{
-		for(i = 0 ; i < errThreshold + 1; i++)
-		{
-			scoreF[0][i] = i;
-			scoreF[i][0] = i;
-		}
-
-
-		rIndex = 1;
-		while(rIndex <= rSeqLength+errThreshold-error1)
-		{
-			tempUp   = (rIndex - ERROR_BOUND) > 0 ? ((rIndex > rSeqLength) ? rSeqLength - ERROR_BOUND :rIndex - ERROR_BOUND) : 1;
-			tempDown = ((rIndex >= rSeqLength- ERROR_BOUND ) ? rSeqLength+1  :rIndex + ERROR_BOUND + 1);
-			for(i = tempUp; i < tempDown ; i++)
-			{
-				errorString = (*(ref+rIndex-1) == *(rSeq+i-1));
-
-				upValue   = scoreF[i-1][rIndex]+1;
-				diagValue = scoreF[i-1][rIndex-1]+ !errorString;
-				sideValue = scoreF[i][rIndex-1]+1;
-
-				if(i != tempUp &&  i != tempDown-1)
-					scoreF[i][rIndex] = min3(sideValue, diagValue , upValue);
-				else if(  (i == ((rIndex - ERROR_BOUND ) > 0 ? rIndex - ERROR_BOUND : 1)) && rIndex <= rSeqLength  )
-					scoreF[i][rIndex] = min(sideValue, diagValue);
-				else if(rIndex > rSeqLength &&  (i == rSeqLength - ERROR_BOUND) )
-					scoreF[i][rIndex] = sideValue;	                    
-				else
-					scoreF[i][rIndex] = min(diagValue , upValue);
-
-				if(i == tempUp)
-					error = scoreF[i][rIndex];
-				if(error > scoreF[i][rIndex])
-					error = scoreF[i][rIndex];
-			}
-			if(rIndex <= rSeqLength)
-			{
-				errorSegment = error;
-			}
-			rIndex++;
-		}
-
-		min  = scoreF[rSeqLength][rSeqLength+errThreshold-error1];
-		minIndex2 = rSeqLength + errThreshold-error1;
-
-		// Find the Best error for all the possible ways.
-		for(i = 1; i <= 2*(errThreshold-error1); i++)
-		{
-			if(min > scoreF[rSeqLength][rSeqLength+errThreshold-error1-i] && rSeqLength+errThreshold-error1-i > 0)
-			{
-				min = scoreF[rSeqLength][rSeqLength+errThreshold-error1-i];
-				minIndex2 = rSeqLength+errThreshold-error1-i;
-			}
-		}
-		error = scoreF[rSeqLength][minIndex2];
-	}
-
-	totalError = error + error1;
-
-
-	if(totalError != error2 + error3 && totalError > errThreshold)
-	{
-		for(i = 0; i < lSeqLength; i++)
-                        printf("%c", *(tempref-1-i));
-                printf("\n");
-                for(i = 0; i < lSeqLength; i++)
-                        printf("%c", *(lSeq+i));
-                printf("\n");
-
-                for(i = 0; i < rSeqLength; i++)
-                        printf("%c", *(tempref+segLength+i));
-                printf("\n");
-
-                for(i = 0; i < rSeqLength; i++)
-                        printf("%c", *(rSeq+i));
-                printf("\n");
-
-
-		printf("SSEF=%d SSEB%d\n", error2, error3);
-		printf("F=%d B=%d\n", error, error1);	
-		scanf("%d", &i);
-	}
-
-	char matrixR[200];
-	char matrixL[200];
-
-	matrixR[0] = '\0';
-	matrixL[0] = '\0';
-
-	size = 0;
-	directionIndex = rSeqLength;
-	rIndex = minIndex2;
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}	
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}	
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixR[size] = *(rSeq+directionIndex-1);
-				size++;
-				matrixR[size] = 'I';
-				directionIndex--;
-			}
-			else if(scoreF[directionIndex][rIndex] - scoreF[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				size++;
-				matrixR[size] = 'D';
-				rIndex--;
-			}
-			else if( scoreF[directionIndex][rIndex] - scoreF[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixR[size] = *(ref+rIndex-1);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixR[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		size++;
-	}
-	matrixR[size] = '\0';	
-
-	size = 0;
-	directionIndex = lSeqLength;
-	rIndex = minIndex1;
-
-
-	while(directionIndex != 0 || rIndex != 0)
-	{
-		if(directionIndex-rIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-
-		}
-		else if(rIndex - directionIndex == errThreshold)
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		else
-		{
-			if(scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex] == 1 && directionIndex != 0)
-			{
-				matrixL[size] = 'I';
-				size++;
-				matrixL[size] = *(lSeq+lSeqLength-directionIndex);
-				directionIndex--;
-			}
-			else if(scoreB[directionIndex][rIndex] - scoreB[directionIndex][rIndex-1] == 1 && rIndex != 0)
-			{
-				matrixL[size] = 'D';
-				size++;
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-			}
-			else if( scoreB[directionIndex][rIndex] - scoreB[directionIndex-1][rIndex-1] == 1 )
-			{
-				matrixL[size] = *(tempref-rIndex);
-				rIndex--;
-				directionIndex--;
-			}
-			else
-			{
-				matrixL[size] = 'M';
-				rIndex--;
-				directionIndex--;
-			}
-		}
-		size++;
-	}
-	matrixL[size] = '\0';
-	char middle[200];
-	middle[0] = '\0';
-	for(i = 0; i < segLength; i++)
-		middle[i] = 'M';
-	middle[segLength] = '\0';
-
-	char rmatrixR[200];
-
-	reverse(matrixR, rmatrixR, strlen(matrixR));
-
-	sprintf(matrix, "%s%s%s", matrixL, middle, rmatrixR);
-	
-	return totalError;
-}
-
-
-int addCigarSize(int cnt){
-  if (cnt<10) return 1;
-  else if (cnt < 100) return 2;
-  return 3;
-}
-
-/*
-	Generate Cigar from the back tracking matrix
-*/
-void generateCigar(char *matrix, int matrixLength, char *cigar)
-{
-	int i = 0;
-
-	int counterM=0;
-	int counterI=0;
-	int counterD=0;
-
-	int cigarSize = 0;
-
-	cigar[0] = '\0';
-	
-	while(i < matrixLength)
-        {
-                if(matrix[i]=='M')
-                {
-                        counterM++;
-                        if(counterI != 0)
-                        {
-			        sprintf(cigar, "%s%dI", cigar, counterI);
-				cigarSize += addCigarSize(counterI) + 1;
-				cigar[cigarSize] = '\0';
-				counterI=0;
-                        }
-			else if(counterD != 0)
-			{
-				sprintf(cigar, "%s%dD", cigar, counterD);
-				cigarSize += addCigarSize(counterD) + 1;
-				cigar[cigarSize] = '\0';
-                                counterD=0;
-			}
-                }
-                else if(matrix[i] == 'I')
-                {
-                        if(counterM != 0)
-                        {
-                                sprintf(cigar, "%s%dM", cigar, counterM);
-				cigarSize += addCigarSize(counterM) + 1;
-				cigar[cigarSize] = '\0';
-                                counterM = 0;
-                        }
-                        else if(counterD != 0)
-                        {
-                              	sprintf(cigar, "%s%dD", cigar, counterD);
-				cigarSize += addCigarSize(counterD) + 1;			  
-				cigar[cigarSize] = '\0';
-                                counterD=0;
-                        }
-			counterI++;
-			i++;
-			
-                }
-		else if (matrix[i] == 'D')
-		{
-			if(counterM != 0)
-                        {
-                                sprintf(cigar, "%s%dM", cigar, counterM);
-				cigarSize += addCigarSize(counterM) + 1;
-				cigar[cigarSize] = '\0';
-                                counterM = 0;
-                        }
-                        else if(counterI != 0)
-                        {
-                                sprintf(cigar, "%s%dI", cigar, counterI);
-				cigarSize += addCigarSize(counterI) + 1;
-				cigar[cigarSize] = '\0';
-                                counterI=0;
-                        }
-			
-			counterD++;
-			i++;
-			
-		}
-		else
-		{
-			counterM++;
-                        if(counterI != 0)
-                        {
-                                sprintf(cigar, "%s%dI", cigar, counterI);
-				cigarSize += addCigarSize(counterI) + 1;
-				cigar[cigarSize] = '\0';
-                                counterI=0;
-                        }
-                        else if(counterD != 0)
-                        {
-                                sprintf(cigar, "%s%dD", cigar, counterD);
-				cigarSize += addCigarSize(counterD) + 1;
-				cigar[cigarSize] = '\0';
-                                counterD=0;
-                        }
-		}
-		i++;
-	}          
-	
-	if(counterM != 0)
-        {
-                sprintf(cigar, "%s%dM", cigar, counterM);
-		cigarSize += addCigarSize(counterM) + 1;
-		cigar[cigarSize] = '\0';
-                counterM = 0;
-        }
-        else if(counterI != 0)
-        {
-                sprintf(cigar, "%s%dI", cigar, counterI);
-		cigarSize += addCigarSize(counterI) + 1;
-		cigar[cigarSize] = '\0';
-                counterI = 0;
-        }
-	else if(counterD != 0)
-	{
-		sprintf(cigar, "%s%dD", cigar, counterD);
-		cigarSize += addCigarSize(counterD) + 1;
-		cigar[cigarSize] = '\0';
-                counterD = 0;
-	}
-	
-	cigar[cigarSize] = '\0';
-}
-
-/*
-	Creates the Cigar output from the mismatching positions format  [0-9]+(([ACTGN]|\^[ACTGN]+)[0-9]+)*
-*/
-void generateCigarFromMD(char *mismatch, int mismatchLength, char *cigar)
-{
-	int i = 0;
-	int j = 0;	
-
-	int start = 0;
-	int cigarSize = 0;
-
-        cigar[0] = '\0';
-
-	while(i < mismatchLength)
-	{
-		if(mismatch[i] >= '0' && mismatch[i] <= '9')
-		{	
-			start = i;
-
-			while(mismatch[i] >= '0' && mismatch[i] <= '9' && i < mismatchLength)
-				i++;					
-
-			int value = atoi(mismatch+start);		
-			for(j = 0;  j < value-1; j++)
-			{
-				cigar[cigarSize] = 'M';	
-				cigarSize++;
-			}
-			cigar[cigarSize] = 'M';
-		}
-		else if(mismatch[i] == '^')
-		{
-			cigar[cigarSize] = 'I';	
-			i++;
-		}
-		else if(mismatch[i] == '\'')
-		{
-			cigar[cigarSize] = 'D';
-			i++;
-		}
-		else
-		{
-			 cigar[cigarSize] = 'M';
-                         cigarSize++;		 
-		}
-		cigarSize++;
-		i++;
-	}
-	cigar[cigarSize] = '\0';
-}
-
-void generateSNPSAM(char *matrix, int matrixLength, char *outputSNP)
-{
-
-	int i = 0;
-
-	int counterM = 0;
-	int counterD = 0;
-
-	char delete[100];
-
-	int snpSize = 0;
-
-	outputSNP[0] = '\0';
-	delete[0] = '\0';
-
-
-	while(i < matrixLength)
-	{
-		if(matrix[i]=='M')
-		{
-			counterM++;		
-			if(counterD != 0)
-			{
-				delete[counterD] = '\0';
-				counterD=0;
-                                sprintf(outputSNP, "%s^%s", outputSNP,delete);
-				snpSize += strlen(delete) + 1;
-				outputSNP[snpSize] = '\0';
-				delete[0] = '\0';
-			}
-		}
-		else if(matrix[i] == 'D')
-		{
-			if(counterM != 0)
-			{
-				sprintf(outputSNP, "%s%d", outputSNP, counterM);	
-				snpSize += addCigarSize(counterM);
-				outputSNP[snpSize] = '\0';
-				counterM=0;
-				delete[counterD] = matrix[i+1];
-				i++;
-				counterD++;
-			}
-			else if(counterD != 0)
-			{
-				delete[counterD] = matrix[i+1];
-				counterD++;
-				i++;
-			}	
-			else
-			{			
-				delete[counterD] = matrix[i+1];
-				counterD++;
-                                i++;
-			}
-		}
-		else if(matrix[i] == 'I')
-		{
-			if(counterM != 0)
-                        {
-			  // sprintf(outputSNP, "%s%d\0", outputSNP, counterM); 
-			  //counterM++;
-                        }                                             
-                        else if(counterD != 0)
-                        {		
-				delete[counterD] = '\0';
-				sprintf(outputSNP, "%s^%s", outputSNP, delete); 
-				snpSize += strlen(delete) + 1;
-				outputSNP[snpSize] = '\0';
- 				counterD = 0;    
-				delete[0] = '\0';                         
-                        }       
-			i++;
-            
-		}
-		else
-		{
-			if(counterM != 0)	
-			{
-				sprintf(outputSNP, "%s%d", outputSNP, counterM);
-				snpSize += addCigarSize(counterM);
-				outputSNP[snpSize] = '\0';
-                                counterM = 0;
-			}
-                        if(counterD != 0)
-                        {
-                                delete[counterD] = '\0';
-                                counterD=0;
-                                sprintf(outputSNP, "%s^%s", outputSNP, delete);
-				snpSize += strlen(delete) + 1;
-				outputSNP[snpSize] = '\0';
-				delete[0] = '\0';
-                        }
-			sprintf(outputSNP,"%s%c",outputSNP,matrix[i]);
-			snpSize += 1;
-			outputSNP[snpSize] = '\0';
-		}
-		i++;
-	}
-	
-	if(counterM != 0)
-        {
-	        sprintf(outputSNP, "%s%d", outputSNP, counterM);
-		snpSize += addCigarSize(counterM);
-		outputSNP[snpSize] = '\0';
-                counterM = 0;
-        }                     
-        else if(counterD != 0)
-        { 
-        	delete[counterD] = '\0';
-                sprintf(outputSNP, "%s^%s", outputSNP, delete);
-		snpSize += strlen(delete) + 1;
-		outputSNP[snpSize] = '\0';
-                counterD = 0;
-        } 
-
-	outputSNP[snpSize] = '\0';
-}
-/**********************************************/
-
-/*
-	direction = 0 forward
-		    1 backward	
-	
-*/
-
-void mapSingleEndSeq(unsigned int *l1, int s1, int readNumber, int readSegment, int direction)
-{
-		int j = 0;
-		int z = 0;
-		int *locs = (int *) l1;
-		char *_tmpSeq, *_tmpQual;
-		char rqual[SEQ_LENGTH+1];
-		rqual[SEQ_LENGTH]='\0';
-
-		int genLoc = 0;
-		int leftSeqLength = 0;
-		int rightSeqLength = 0;
-		int middleSeqLength = 0; 
-
-		char matrix[200];
-		char editString[200];
-		char cigar[MAX_CIGAR_SIZE];
-
-		short *_tmpHashValue;
-
-		if (direction)
-		{
-			reverse(_msf_seqList[readNumber].qual, rqual, SEQ_LENGTH);
-			_tmpQual = rqual;
-			_tmpSeq = _msf_seqList[readNumber].rseq;
-			_tmpHashValue = _msf_seqList[readNumber].rhashValue;
-		}
-		else
-		{
-			_tmpQual = _msf_seqList[readNumber].qual;
-			_tmpSeq = _msf_seqList[readNumber].seq;
-                        _tmpHashValue = _msf_seqList[readNumber].hashValue;
-		}
-
-		int readId = 2*readNumber+direction;
-		for (z=0; z<s1; z++)
-		{
-
-			
-			int map_location = 0;
-			int a = 0;
-			int o = readSegment;
-
-			genLoc = locs[z];//-_msf_samplingLocs[o];
-			
-
-			if ( genLoc-_msf_samplingLocs[o] < _msf_refGenBeg || 
-			     genLoc-_msf_samplingLocs[o] > _msf_refGenEnd ||
-			     _msf_verifiedLocs[genLoc-_msf_samplingLocs[o]] == readId || 
-  			     _msf_verifiedLocs[genLoc-_msf_samplingLocs[o]] == -readId 
-			   )
-				continue;
-			int err = -1;
-			
-
-			map_location = 0;                        
-
-			leftSeqLength = _msf_samplingLocs[o];
-			middleSeqLength = WINDOW_SIZE;
-			a = leftSeqLength + middleSeqLength;
-			rightSeqLength = SEQ_LENGTH - a;
-
-			if(errThreshold == 2)
-				 err = verifySingleEndEditDistance2(genLoc, _tmpSeq, leftSeqLength,
-								   _tmpSeq + a, rightSeqLength,
-								  middleSeqLength, matrix, &map_location, _tmpHashValue);
-			else if(errThreshold == 4)
-				err = verifySingleEndEditDistance4(genLoc, _tmpSeq, leftSeqLength,
-								   _tmpSeq + a, rightSeqLength,
-								  middleSeqLength, matrix, &map_location, _tmpHashValue);
-			else if(errThreshold ==3)
-				err = verifySingleEndEditDistance(genLoc, _tmpSeq, leftSeqLength,
-                                                                   _tmpSeq + a, rightSeqLength,
-                                                                  middleSeqLength, matrix, &map_location, _tmpHashValue);
-			/*else if(errThreshold == 6)
-				err = verifySingleEndEditDistance(genLoc, _tmpSeq, leftSeqLength,
-								   _tmpSeq + a, rightSeqLength,
-								  middleSeqLength, matrix, &map_location, _tmpHashValue);
-			*/
-			else
-				err = verifySingleEndEditDistanceExtention(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);
-
-			if(err != -1)
-			{
-				generateSNPSAM(matrix, strlen(matrix), editString);
-				generateCigar(matrix, strlen(matrix), cigar);
-			}
-			
-			if(err != -1 && !bestMode)
-			{
-				
-				mappingCnt++;
-
-				int j = 0;
-				int k = 0;
-				for(k = 0; k < readSegment+1; k++)
-				{
-					for(j = -errThreshold ; j <= errThreshold; j++) 
-					{
-						if(genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j >= _msf_refGenBeg &&
-						   genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j <= _msf_refGenEnd)
-							_msf_verifiedLocs[genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j] = readId;
-					}
-				}
-				_msf_seqList[readNumber].hits[0]++;
-
-				_msf_output.QNAME		= _msf_seqList[readNumber].name;
-				_msf_output.FLAG		= 16 * direction;
-				_msf_output.RNAME		= _msf_refGenName;
-				_msf_output.POS			= map_location + _msf_refGenOffset;
-				_msf_output.MAPQ		= 255;
-				_msf_output.CIGAR		= cigar;
-				_msf_output.MRNAME		= "*";
-				_msf_output.MPOS		= 0;
-				_msf_output.ISIZE		= 0;
-				_msf_output.SEQ			= _tmpSeq;
-				_msf_output.QUAL		= _tmpQual;
-
-				_msf_output.optSize		= 2;
-				_msf_output.optFields	= _msf_optionalFields;
-
-				_msf_optionalFields[0].tag = "NM";
-				_msf_optionalFields[0].type = 'i';
-				_msf_optionalFields[0].iVal = err;
-
-				_msf_optionalFields[1].tag = "MD";
-				_msf_optionalFields[1].type = 'Z';
-				_msf_optionalFields[1].sVal = editString;
-
-				output(_msf_output);
-
-
-				if (_msf_seqList[readNumber].hits[0] == 1)
-				{
-					mappedSeqCnt++;
-				}
-
-				if ( maxHits == 0 )
-				{
-					_msf_seqList[readNumber].hits[0] = 2;
-				}
-
-
-				if ( maxHits!=0 && _msf_seqList[readNumber].hits[0] == maxHits)
-				{
-					completedSeqCnt++;
-					break;
-				}
-
-			}
-			else if(err != -1 && bestMode)
-			{
-				mappingCnt++;
-				_msf_seqList[readNumber].hits[0]++;
-
-				if (_msf_seqList[readNumber].hits[0] == 1)
-				{
-					mappedSeqCnt++;
-				}
-
-				if ( maxHits == 0 )
-				{
-					_msf_seqList[readNumber].hits[0] = 2;
-				}
-
-				if(err  < bestHitMappingInfo[readNumber].err || bestHitMappingInfo[readNumber].loc == -1)
-				{
-					setFullMappingInfo(readNumber, map_location + _msf_refGenOffset, direction, err, 0, editString, _msf_refGenName, cigar );
-				}
-			}
-			else
-			{
-				for(j = -errThreshold ; j <= errThreshold; j++)
-				{
-					if(genLoc+j > _msf_refGenBeg &&
-					   genLoc+j < _msf_refGenEnd)
-						_msf_verifiedLocs[genLoc+j] = -readId;
-				}
-			}
-		}
-}
-
-
-int mapAllSingleEndSeq()
-{
-	int i = 0;
-	int j = 0;
-	int k  = 0;
-
-	
-	unsigned int *locs = NULL;
-	
-
-	int prev_hash = 0;
-	
-	for(i = 0; i < _msf_seqListSize; i++)
-	{
-		for(j = 0; j < _msf_samplingLocsSize; j++)
-		{
-			k = _msf_sort_seqList[i].readNumber;
-//			if(j != 0)
-//				if(strncmp(_msf_seqList[k].seq+_msf_samplingLocs[j], _msf_seqList[k].seq+_msf_samplingLocs[j-1], segSize) == 0)
-//					continue;
-//			if(prev_hash ==  hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]))
-//				continue;
-			locs = getCandidates ( hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]));
-			if ( locs != NULL)
-			{
-				mapSingleEndSeq(locs+1, locs[0],k ,j, 0);		
-			}
-			prev_hash = hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]);
-		}
-	}
-	i = 0;
-	
-	for(i = 0; i < _msf_seqListSize; i++)
-	{
-		for(j = 0; j < _msf_samplingLocsSize; j++)
-		{
-			k = _msf_sort_seqList[i].readNumber;
-
-//			if(j != 0)
-//				if(strncmp(_msf_seqList[k].rseq+_msf_samplingLocs[j], _msf_seqList[k].rseq+_msf_samplingLocs[j-1], segSize) == 0)
-//					continue;
-//			if(prev_hash ==  hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]))
-//				continue;
-			locs = getCandidates ( hashVal(_msf_seqList[k].rseq+_msf_samplingLocs[j]));
-			if ( locs != NULL)
-			{
-				mapSingleEndSeq(locs+1, locs[0],k ,j, 1);
-			}
-			prev_hash = hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]);
-		}
-	}
-	return 1;
-}
-
-
-/**********************************************/
-/**********************************************/
-/**********************************************/
-/**********************************************/
-/**********************************************/
-int compareOut (const void *a, const void *b)
-{
-	FullMappingInfo *aInfo = (FullMappingInfo *)a;
-	FullMappingInfo *bInfo = (FullMappingInfo *)b;
-	return aInfo->loc - bInfo->loc;
-}
-
-
-
-/**********************************************/
-
-/*
-	direction 0: Forward
-		  1: Reverse
-*/
-
-void mapPairEndSeqList(unsigned int *l1, int s1, int readNumber, int readSegment, int direction)
-{
-		int z = 0;
-		int *locs = (int *) l1;
-		char *_tmpSeq;
-
-		char rqual[SEQ_LENGTH+1];
-
-		char matrix[200];
-		char editString[200];
-		char cigar[MAX_CIGAR_SIZE];
-
-		short *_tmpHashValue;
-	
-		int leftSeqLength = 0;
-		int middleSeqLength = 0;
-		int rightSeqLength =0;
-		int a = 0;
-
-		rqual[SEQ_LENGTH]='\0';
-
-
-		int r = readNumber;
-	
-		char d = (direction==1)?-1:1;
-
-		if (d==-1)
-		{
-			_tmpSeq = _msf_seqList[readNumber].rseq;
-			_tmpHashValue = _msf_seqList[r].rhashValue;
-		}
-		else
-		{
-			_tmpSeq = _msf_seqList[readNumber].seq;
-			_tmpHashValue = _msf_seqList[r].hashValue;
-		}
-
-		int readId = 2*readNumber+direction;
-		for (z=0; z<s1; z++)
-		{
-			int genLoc = locs[z];//-_msf_samplingLocs[o];                   
-			int err = -1;
-			int map_location = 0;
-			int o = readSegment;
-
-			leftSeqLength = _msf_samplingLocs[o];
-			middleSeqLength = WINDOW_SIZE;
-			a = leftSeqLength + middleSeqLength;
-			rightSeqLength = SEQ_LENGTH - a;
-			
-			if(genLoc - leftSeqLength < _msf_refGenBeg || genLoc + rightSeqLength + middleSeqLength > _msf_refGenEnd ||
-			   _msf_verifiedLocs[genLoc-_msf_samplingLocs[o]] == readId || _msf_verifiedLocs[genLoc-_msf_samplingLocs[o]] == -readId)
-				continue;
-
-			if(errThreshold == 2)
-				err = verifySingleEndEditDistance2(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);
-			else if(errThreshold == 4)
-				err = verifySingleEndEditDistance4(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);
-			else if(errThreshold ==3)
-				err = verifySingleEndEditDistance(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);
-			/*else if(errThreshold == 6)
-				err = verifySingleEndEditDistance(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);*/
-			else
-				err = verifySingleEndEditDistanceExtention(genLoc, _tmpSeq, leftSeqLength,
-						_tmpSeq + a, rightSeqLength,
-						middleSeqLength, matrix, &map_location, _tmpHashValue);
-
-			
-			if (err != -1)
-			{
-				int j = 0;
-				int k = 0;
-
-				for(k = 0; k < readSegment+1; k++)
-				{
-					for(j = -errThreshold ; j <= errThreshold; j++)
-					{
-						if(genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j >= _msf_refGenBeg &&
-								genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j <= _msf_refGenEnd)
-							_msf_verifiedLocs[genLoc-(k*(_msf_samplingLocs[1]-_msf_samplingLocs[0]))+j] = readId;
-					}
-				}
-
-
-				generateSNPSAM(matrix, strlen(matrix), editString);
-				generateCigar(matrix, strlen(matrix), cigar);
-
-				MappingLocations *parent = NULL;
-				MappingLocations *child = _msf_mappingInfo[r].next;
-					
-				genLoc = map_location + _msf_refGenOffset;
-				int i = 0;
-				for (i=0; i<(_msf_mappingInfo[r].size/MAP_CHUNKS); i++)
-				{
-					parent = child;
-					child = child->next;
-				}
-
-				if (child==NULL)
-				{
-					MappingLocations *tmp = getMem(sizeof(MappingLocations));
-
-					tmp->next = NULL;
-					tmp->loc[0]=genLoc * d;
-					tmp->err[0]=err; 
-
-					tmp->cigarSize[0] = strlen(cigar);
-					sprintf(tmp->cigar[0],"%s", cigar);
-
-					tmp->mdSize[0] = strlen(editString);
-					sprintf(tmp->md[0],"%s", editString);
-
-					if (parent == NULL)
-						_msf_mappingInfo[r].next = tmp;
-					else
-						parent->next = tmp;
-				}
-				else
-				{
-					if(strlen(cigar) > SEQ_LENGTH || strlen(editString) > SEQ_LENGTH)
-					{
-					  printf("ERROR in %d read size(After mapping) exceedes cigar=%d md =%d cigar=%s md =%s\n", r,  (int)strlen(cigar), (int)strlen(editString), cigar, editString);
-					}
-
-					child->loc[_msf_mappingInfo[r].size % MAP_CHUNKS] = genLoc * d;
-					child->err[_msf_mappingInfo[r].size % MAP_CHUNKS] = err;	
-
-					child->cigarSize[_msf_mappingInfo[r].size % MAP_CHUNKS] = strlen(cigar);
-					sprintf(child->cigar[_msf_mappingInfo[r].size % MAP_CHUNKS],"%s",cigar);
-					
-					child->mdSize[_msf_mappingInfo[r].size % MAP_CHUNKS] = strlen(editString);
-					sprintf(child->md[_msf_mappingInfo[r].size % MAP_CHUNKS],"%s",editString);
-				}
-				_msf_mappingInfo[r].size++;
-
-			}
-			else	
-			{
-				_msf_verifiedLocs[genLoc] = -readId;
-			}
-
-		}
-}
-
-/**********************************************/
-void mapPairedEndSeq()
-{
-	int i = 0;
-	int j = 0;
-	int k = 0;
-
-	unsigned int *locs = NULL;
-	while ( i < _msf_seqListSize )
-	{
-		for(j = 0; j < _msf_samplingLocsSize; j++)
-		{
-			k = _msf_sort_seqList[i].readNumber;
-			locs = getCandidates ( hashVal(_msf_seqList[k].seq+_msf_samplingLocs[j]));
-			if ( locs != NULL)
-			{
-				mapPairEndSeqList(locs+1, locs[0],k ,j, 0);
-			}
-		}
-		i++;
-	}
-	i = 0;
-
-	while ( i < _msf_seqListSize )
-	{
-		for(j = 0; j < _msf_samplingLocsSize; j++)
-		{
-			k = _msf_sort_seqList[i].readNumber;
-			locs = getCandidates ( hashVal(_msf_seqList[k].rseq+_msf_samplingLocs[j]));
-			if ( locs != NULL)
-			{
-				mapPairEndSeqList(locs+1, locs[0],k ,j, 1);
-			}
-		}
-
-		i++;
-	}
-	char fname1[FILE_NAME_LENGTH];
-	char fname2[FILE_NAME_LENGTH];
-	MappingLocations *cur; 
-	int tmpOut;
-	int lmax=0, rmax=0;
-
-	sprintf(fname1, "%s__%s__%s__%d__1.tmp",mappingOutputPath, _msf_refGenName, mappingOutput, _msf_openFiles);
-	sprintf(fname2, "%s__%s__%s__%d__2.tmp",mappingOutputPath, _msf_refGenName, mappingOutput, _msf_openFiles);
-
-	FILE* out;
-	FILE* out1 = fileOpen(fname1, "w");
-	FILE* out2 = fileOpen(fname2, "w");
-
-	_msf_openFiles++;
-
-	for (i=0; i<_msf_seqListSize; i++)
-	{
-
-		if (i%2==0)
-		{
-			out = out1;
-
-			if (lmax <  _msf_mappingInfo[i].size)
-			{
-				lmax = _msf_mappingInfo[i].size;
-			}
-		}
-		else
-		{
-			out = out2;
-			if (rmax < _msf_mappingInfo[i].size)
-			{	
-				rmax = _msf_mappingInfo[i].size;
-			}
-		}
-
-		tmpOut = fwrite(&(_msf_mappingInfo[i].size), sizeof(int), 1, out);					
-		if (_msf_mappingInfo[i].size > 0)
-		{
-			cur = _msf_mappingInfo[i].next;
-			for (j=0; j < _msf_mappingInfo[i].size; j++)
-			{
-				if ( j>0  && j%MAP_CHUNKS==0)
-				{
-					cur = cur->next;
-				}
-				if(cur->cigarSize[j % MAP_CHUNKS] > SEQ_LENGTH || cur->mdSize[j % MAP_CHUNKS] > SEQ_LENGTH)
-				{
-					printf("ERROR in %d read size exceeds cigar=%d md =%d cigar=%s md =%s\n", i,  cur->cigarSize[j % MAP_CHUNKS], cur->mdSize[j % MAP_CHUNKS], cur->cigar[j % MAP_CHUNKS], cur->md[j % MAP_CHUNKS]);	
-				}
-				
-				tmpOut = fwrite(&(cur->loc[j % MAP_CHUNKS]), sizeof(int), 1, out);
-
-				tmpOut = fwrite(&(cur->err[j % MAP_CHUNKS]), sizeof(int), 1, out);
-				
-				tmpOut = fwrite(&(cur->cigarSize[j % MAP_CHUNKS]), sizeof(int), 1, out);
-				tmpOut = fwrite((cur->cigar[j % MAP_CHUNKS]), sizeof(char), (cur->cigarSize[j % MAP_CHUNKS]), out);
-				
-				tmpOut = fwrite(&(cur->mdSize[j % MAP_CHUNKS]), sizeof(int), 1, out);
-				tmpOut = fwrite((cur->md[j % MAP_CHUNKS]), sizeof(char), (cur->mdSize[j % MAP_CHUNKS]), out);
-	
-			}
-			_msf_mappingInfo[i].size = 0;
-			//_msf_mappingInfo[i].next = NULL;
-		}
-	}
-
-	_msf_maxLSize += lmax;
-	_msf_maxRSize += rmax;
-
-	fclose(out1);
-	fclose(out2);
-
-}
-
-void outputPairFullMappingInfo(FILE *fp, int readNumber)
-{
-
-	char *seq1, *seq2, *rseq1, *rseq2, *qual1, *qual2;
-	char rqual1[SEQ_LENGTH+1], rqual2[SEQ_LENGTH+1];
-
-	rqual1[SEQ_LENGTH] = rqual2[SEQ_LENGTH] = '\0';
-	
-	seq1 = _msf_seqList[readNumber*2].seq;
-	rseq1 = _msf_seqList[readNumber*2].rseq;
-	qual1 = _msf_seqList[readNumber*2].qual;
-
-	reverse(_msf_seqList[readNumber*2].qual, rqual1, SEQ_LENGTH);
-
-	seq2 = _msf_seqList[readNumber*2+1].seq;
-	rseq2 = _msf_seqList[readNumber*2+1].rseq;
-	qual2 = _msf_seqList[readNumber*2+1].qual;
-
-	reverse(_msf_seqList[readNumber*2+1].qual, rqual2, SEQ_LENGTH);
-
-
-	if(bestHitMappingInfo[readNumber*2].loc == -1 && bestHitMappingInfo[readNumber*2+1].loc == -1)
-		return;
-	else
-	{
-
-		char *seq;
-		char *qual;
-		char d1;
-		char d2;
-		int isize;
-		int proper=0;
-		// ISIZE CALCULATION
-		// The distance between outer edges                                                             
-		isize = abs(bestHitMappingInfo[readNumber*2].loc - bestHitMappingInfo[readNumber*2+1].loc)+SEQ_LENGTH - 2;                                              
-
-		if (bestHitMappingInfo[readNumber*2].loc - bestHitMappingInfo[readNumber*2+1].loc > 0)
-		{
-			isize *= -1;
-		}
-		d1 = (bestHitMappingInfo[readNumber*2].dir == -1)?1:0;
-		d2 = (bestHitMappingInfo[readNumber*2+1].dir == -1)?1:0;
-
-		if ( d1 )
-		{
-			seq = rseq1;
-			qual = rqual1;
-		}
-		else
-		{
-			seq = seq1;
-			qual = qual1;
-		}
-		if ( (bestHitMappingInfo[readNumber*2].loc < bestHitMappingInfo[readNumber*2+1].loc && !d1 && d2) ||
-			 (bestHitMappingInfo[readNumber*2].loc > bestHitMappingInfo[readNumber*2+1].loc && d1 && !d2) )
-		{
-			proper = 2;
-		}
-		else
-		{
-			proper = 0;
-		}
-
-		_msf_output.POS                 = bestHitMappingInfo[readNumber*2].loc;
-		_msf_output.MPOS                = bestHitMappingInfo[readNumber*2+1].loc;
-		_msf_output.FLAG                = 1+proper+16*d1+32*d2+64;
-		_msf_output.ISIZE               = isize;
-		_msf_output.SEQ                 = seq,
-		_msf_output.QUAL                = qual;
-		_msf_output.QNAME               = _msf_seqList[readNumber*2].name;
-		_msf_output.RNAME               = bestHitMappingInfo[readNumber*2].chr;
-		_msf_output.MAPQ                = 255;
-		_msf_output.CIGAR               = bestHitMappingInfo[readNumber*2].cigar;
-		_msf_output.MRNAME              = "=";
-
-		_msf_output.optSize     = 2;
-		_msf_output.optFields   = _msf_optionalFields;
-
-		_msf_optionalFields[0].tag = "NM";
-		_msf_optionalFields[0].type = 'i';
-		_msf_optionalFields[0].iVal = bestHitMappingInfo[readNumber*2].err;
-
-		_msf_optionalFields[1].tag = "MD";
-		_msf_optionalFields[1].type = 'Z';
-		_msf_optionalFields[1].sVal = bestHitMappingInfo[readNumber*2].md;
-
-		outputSAM(fp, _msf_output);
-		output(_msf_output);
-
-		if ( d2 )
-		{
-			seq = rseq2;
-			qual = rqual2;
-		}
-		else
-		{
-			seq = seq2;
-			qual = qual2;
-		}
-
-		_msf_output.POS                 = bestHitMappingInfo[readNumber*2+1].loc;
-		_msf_output.MPOS                = bestHitMappingInfo[readNumber*2].loc;
-		_msf_output.FLAG                = 1+proper+16*d2+32*d1+128;
-		_msf_output.ISIZE               = -isize;
-		_msf_output.SEQ                 = seq,
-		_msf_output.QUAL                = qual;
-		_msf_output.QNAME               = _msf_seqList[readNumber*2].name;
-		_msf_output.RNAME               = bestHitMappingInfo[readNumber*2].chr;
-		_msf_output.MAPQ                = 255;
-		_msf_output.CIGAR               = bestHitMappingInfo[readNumber*2+1].cigar;
-		_msf_output.MRNAME              = "=";
-
-		_msf_output.optSize     = 2;
-		_msf_output.optFields   = _msf_optionalFields;
-
-		_msf_optionalFields[0].tag = "NM";
-		_msf_optionalFields[0].type = 'i';
-		_msf_optionalFields[0].iVal = bestHitMappingInfo[readNumber*2+1].err;
-
-		_msf_optionalFields[1].tag = "MD";
-		_msf_optionalFields[1].type = 'Z';
-		_msf_optionalFields[1].sVal = bestHitMappingInfo[readNumber*2+1].md;
-
-		outputSAM(fp, _msf_output);
-		output(_msf_output);
-	}
-}
-
-
-/*
-Find the closet one to the c
- @return 0: if the x1 is closer to c 
-	 1: if the x2 is closer to c 	 
-	 2: if both distance are equal
-	 -1: if error
-*/
-int findNearest(int x1, int x2, int c)
-{
-
-	if (abs(x1 - c) > abs(x2 - c) )
-		return 0;
-	else if ( abs(x1 - c) <  abs(x2 - c) )
-		return 1;
-	else if ( abs(x1 - c) == abs(x2 - c) )
-		return 2;
-	else
-		return -1;
-}
-
-void initBestConcordantDiscordant(int readNumber)
-{
-        char bestConcordantFileName[FILE_NAME_LENGTH];
-        char bestDiscordantFileName[FILE_NAME_LENGTH];
-
-	//OPEN THE BEST CONCORDANT FILE
-        //BEGIN{Farhad Hormozdiari}
-        sprintf(bestConcordantFileName, "%s%s__BEST.CONCORDANT", mappingOutputPath, mappingOutput);
-        bestConcordantFILE = fileOpen(bestConcordantFileName, "w");
-        //END{Farhad Hormozdiari}
-
-
-        //OPEN THE BEST DISCORDANT FILE
-        //BEGIN{Farhad Hormozdiari}
-        sprintf(bestDiscordantFileName, "%s%s__BEST.DISCORDANT", mappingOutputPath, mappingOutput);
-        bestDiscordantFILE = fileOpen(bestDiscordantFileName, "w");
-        //END{Farhad Hormozdiari}
-	
-	initBestMapping(readNumber);
-}
-
-void finalizeBestConcordantDiscordant()
-{
-	int i = 0; 
-	
-	for(i = 0;  i<_msf_seqListSize/2; i++)
-	{
-		if(_msf_readHasConcordantMapping[i]==1)
-			outputPairFullMappingInfo(bestConcordantFILE, i);
-		else
-			outputPairFullMappingInfo(bestDiscordantFILE, i);
-	}	
-	
-	fclose(bestConcordantFILE);
-	fclose(bestDiscordantFILE);
-
-	freeMem(bestHitMappingInfo, _msf_seqListSize * sizeof(FullMappingInfo));
-}
-
-void setFullMappingInfo(int readNumber, int loc, int dir, int err, int score, char *md, char * refName, char *cigar)
-{
-	bestHitMappingInfo[readNumber].loc   = loc;
-	bestHitMappingInfo[readNumber].dir   = dir;
-	bestHitMappingInfo[readNumber].err   = err;
-	bestHitMappingInfo[readNumber].score = score;
-
-	strncpy(bestHitMappingInfo[readNumber].md,  md, strlen(md));
-	strncpy(bestHitMappingInfo[readNumber].chr, refName, strlen(refName));
-	strncpy(bestHitMappingInfo[readNumber].cigar, cigar, strlen(cigar));
-}
-
-
-void setPairFullMappingInfo(int readNumber, FullMappingInfo mi1, FullMappingInfo mi2)
-{
-
-	bestHitMappingInfo[readNumber*2].loc   = mi1.loc;
-	bestHitMappingInfo[readNumber*2].dir   = mi1.dir;
-	bestHitMappingInfo[readNumber*2].err   = mi1.err;
-	bestHitMappingInfo[readNumber*2].score = mi1.score;
-	snprintf(bestHitMappingInfo[readNumber*2].chr, MAX_REF_SIZE, "%s", _msf_refGenName);
-	
-	strncpy(bestHitMappingInfo[readNumber*2].md, mi1.md, strlen(mi1.md));
-	strncpy(bestHitMappingInfo[readNumber*2].cigar, mi1.cigar, strlen(mi1.cigar));
-
-	/*
-	sprintf(bestHitMappingInfo[readNumber*2].md, "%s\0",  mi1.md);
-	sprintf(bestHitMappingInfo[readNumber*2].cigar, "%s\0", mi1.cigar);
-	*/
-
-
-	bestHitMappingInfo[readNumber*2+1].loc   = mi2.loc;
-	bestHitMappingInfo[readNumber*2+1].dir   = mi2.dir;
-	bestHitMappingInfo[readNumber*2+1].err   = mi2.err;
-	bestHitMappingInfo[readNumber*2+1].score = mi2.score;
-
-	snprintf(bestHitMappingInfo[readNumber*2+1].chr, MAX_REF_SIZE, "%s", _msf_refGenName);
-
-	/*
-	sprintf(bestHitMappingInfo[readNumber*2+1].md, "%s\0", mi2.md);
-	sprintf(bestHitMappingInfo[readNumber*2+1].cigar, "%s\0", mi2.cigar);
-	*/
-	
-	strncpy(bestHitMappingInfo[readNumber*2+1].md, mi2.md, strlen(mi2.md));
-	strncpy(bestHitMappingInfo[readNumber*2+1].cigar, mi2.cigar, strlen(mi2.cigar));
-	
-}
-
-/**********************************************/
-void outputPairedEnd()
-{
-	int i = 0;
-
-	char cigar[MAX_CIGAR_SIZE];
-
-	int tmpOut;
-	
-	loadRefGenome(&_msf_refGen, &_msf_refGenName, &tmpOut);
-
-	FILE* in1[_msf_openFiles];
-	FILE* in2[_msf_openFiles];
-
-	char fname1[_msf_openFiles][FILE_NAME_LENGTH];	
-	char fname2[_msf_openFiles][FILE_NAME_LENGTH];	
-
-	// discordant
-	FILE *out=NULL, *out1=NULL;
-
-	char fname3[FILE_NAME_LENGTH];
-	char fname4[FILE_NAME_LENGTH];
-	
-	int meanDistanceMapping = 0;
-
-	char *rqual1;
-	char *rqual2;
-
-	rqual1 = getMem((SEQ_LENGTH+1)*sizeof(char));		
-	rqual2 = getMem((SEQ_LENGTH+1)*sizeof(char));		
-
-	if (pairedEndDiscordantMode)
-	{
-		sprintf(fname3, "%s__%s__disc", mappingOutputPath, mappingOutput);
-		sprintf(fname4, "%s__%s__oea", mappingOutputPath, mappingOutput);
-		out = fileOpen(fname3, "a");
-		out1 = fileOpen(fname4, "a");
-	}
-
-	FullMappingInfo *mi1 = getMem(sizeof(FullMappingInfo) * _msf_maxLSize);
-	FullMappingInfo *mi2 = getMem(sizeof(FullMappingInfo) * _msf_maxRSize);
-
-	_msf_fileCount[_msf_maxFile] = 0;
-	for (i=0; i<_msf_openFiles; i++)
-	{
-		sprintf(fname1[i], "%s__%s__%s__%d__1.tmp", mappingOutputPath, _msf_refGenName, mappingOutput, i);
-		sprintf(_msf_fileName[_msf_maxFile][_msf_fileCount[_msf_maxFile]][0], "%s", fname1[i]);
-
-		sprintf(fname2[i], "%s__%s__%s__%d__2.tmp", mappingOutputPath, _msf_refGenName, mappingOutput, i);
-		sprintf(_msf_fileName[_msf_maxFile][_msf_fileCount[_msf_maxFile]][1], "%s", fname2[i]);
-
-		in1[i] = fileOpen(fname1[i], "r");
-		in2[i] = fileOpen(fname2[i], "r");
-		_msf_fileCount[_msf_maxFile]++;
-	}
-	_msf_maxFile++;
-
-	int size;
-	int j, k;
-	int size1, size2;
-
-	meanDistanceMapping = (pairedEndDiscordantMode==1)? (minPairEndedDiscordantDistance+maxPairEndedDiscordantDistance)/2 + SEQ_LENGTH 
-																	  : (minPairEndedDistance + maxPairEndedDistance) / 2 + SEQ_LENGTH;
-
-	for (i=0; i<_msf_seqListSize/2; i++)
-	{
-		size1 = size2 = 0;
-		for (j=0; j<_msf_openFiles; j++)
-		{
-			tmpOut = fread(&size, sizeof(int), 1, in1[j]);
-			if ( size > 0 )
-			{
-				for (k=0; k<size; k++)
-				{
-					mi1[size1+k].dir = 1;
-					tmpOut = fread (&(mi1[size1+k].loc), sizeof(int), 1, in1[j]);
-					tmpOut = fread (&(mi1[size1+k].err), sizeof(int), 1, in1[j]);
-					
-					tmpOut = fread (&(mi1[size1+k].cigarSize), sizeof(int), 1, in1[j]);
-					tmpOut = fread ((mi1[size1+k].cigar), sizeof(char), mi1[size1+k].cigarSize, in1[j]);
-					mi1[size1+k].cigar[mi1[size1+k].cigarSize] = '\0';
-					
-					tmpOut = fread (&(mi1[size1+k].mdSize), sizeof(int), 1, in1[j]);
-					tmpOut = fread ((mi1[size1+k].md), sizeof(char), (mi1[size1+k].mdSize), in1[j]);
-					mi1[size1+k].md[mi1[size1+k].mdSize] = '\0';
-					
-					if (mi1[size1+k].loc<1)
-					{	
-						mi1[size1+k].loc *= -1;
-						mi1[size1+k].dir = -1;
-					}
-				}
-				qsort(mi1+size1, size, sizeof(FullMappingInfo), compareOut);
-				size1+=size;
-			}
-		}
-
-		for (j=0; j<_msf_openFiles; j++)
-		{
-			tmpOut = fread(&size, sizeof(int), 1, in2[j]);
-			if ( size > 0 )
-			{
-				for (k=0; k<size; k++)
-				{
-					mi2[size2+k].dir = 1;
-					tmpOut = fread (&(mi2[size2+k].loc), sizeof(int), 1, in2[j]);
-					tmpOut = fread (&(mi2[size2+k].err), sizeof(int), 1, in2[j]);
-					
-					tmpOut = fread (&(mi2[size2+k].cigarSize), sizeof(int), 1, in2[j]);
-					tmpOut = fread ((mi2[size2+k].cigar), sizeof(char), mi2[size2+k].cigarSize, in2[j]);
-					mi2[size2+k].cigar[mi2[size2+k].cigarSize] = '\0';
-					
-					tmpOut = fread (&(mi2[size2+k].mdSize), sizeof(int), 1, in2[j]);
-					tmpOut = fread ((mi2[size2+k].md), sizeof(char), mi2[size2+k].mdSize, in2[j]);
-					mi2[size2+k].md[mi2[size2+k].mdSize] = '\0';
-					
-					if (mi2[size2+k].loc<1)
-					{	
-						mi2[size2+k].loc *= -1;
-						mi2[size2+k].dir = -1;
-					}
-				}
-				qsort(mi2+size2, size, sizeof(FullMappingInfo), compareOut);
-				size2+=size;
-			}
-		}
-
-		int lm, ll, rl, rm;
-		int pos = 0;
-
-		if (pairedEndDiscordantMode)
-		{
-			
-			for (j=0; j<size1; j++)
-			{
-				lm = mi1[j].loc - maxPairEndedDiscordantDistance + 1;
-				ll = mi1[j].loc - minPairEndedDiscordantDistance + 1;
-				rl = mi1[j].loc + minPairEndedDiscordantDistance - 1;
-				rm = mi1[j].loc + maxPairEndedDiscordantDistance - 1;
-
-				while (pos<size2 && mi2[pos].loc < lm)
-				{
-					pos++;
-				}
-
-				k = pos;
-				while (k<size2 && mi2[k].loc<=rm)
-				{
-					if ( mi2[k].loc <= ll || mi2[k].loc >= rl)
-					{
-						if ( (mi1[j].loc < mi2[k].loc && mi1[j].dir==1 && mi2[k].dir == -1)  ||  
-							 (mi1[j].loc > mi2[k].loc && mi1[j].dir==-1 && mi2[k].dir == 1) )
-						{
-							_msf_seqList[i*2].hits[0]=1;
-							_msf_seqList[i*2+1].hits[0]=1;
-							
-							if(nosamMode != 0)
-							{
-								size1=0;
-								size2=0;
-							}
-
-							break;
-						}
-					}
-					k++;
-				}
-			}
-
-			_msf_seqHits[i*2] += size1;
-			_msf_seqHits[i*2+1] += size2;
-			
-
-			if (_msf_seqHits[i*2+1] * _msf_seqHits[i*2] > DISCORDANT_CUT_OFF && nosamMode != 0)
-			{
-				_msf_seqList[i*2].hits[0]=1;
-				_msf_seqList[i*2+1].hits[0]=1;
-				size1=0;
-				size2=0;
-			}
-
-			
-
-			
-			int tmp = 0;
-			int rNo = 0;
-			int loc = 0;
-			int err = 0;
-			float sc = 0;
-			char l = 0;
-				
-			//write the OEA data
-			if(_msf_seqHits[i*2] == 0 )
-			{
-				for(k = 0;k < size2 && _msf_oeaMapping[i*2+1] < maxOEAOutput ;k++)
-				{
-					rNo = i*2+1;
-					loc = mi2[k].loc*mi2[k].dir;
-					err = mi2[k].err;
-					sc = mi2[k].score;
-
-					l = strlen(_msf_refGenName);
-
-					tmp = fwrite(&rNo, sizeof(int), 1, out1);
-
-					tmp = fwrite(&l, sizeof(char), 1, out1);
-					tmp = fwrite(_msf_refGenName, sizeof(char), l, out1);
-
-					tmp = fwrite(&loc, sizeof(int), 1, out1);
-					tmp = fwrite(&err, sizeof(int), 1, out1);
-					tmp = fwrite(&sc, sizeof(float), 1, out1);
-
-					if(mi2[k].cigarSize > SEQ_LENGTH || mi2[k].cigarSize <= 0)
-						printf("ERROR  CIGAR size=%d %s\n", mi2[k].cigarSize, _msf_seqList[i*2+1].seq);
-					
-					tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out1);
-					tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out1);
-					
-					tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out1);
-					tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out1);
-					
-					_msf_oeaMapping[i*2+1]++;
-				}
-			}
-			if(_msf_seqHits[i*2+1] == 0)
-			{
-				for(j = 0;j < size1 && _msf_oeaMapping[i*2] < maxOEAOutput;j++)
-				{
-					rNo = i*2;
-					loc = mi1[j].loc*mi1[j].dir;
-					err = mi1[j].err;
-					sc = mi1[j].score;
-
-					l = strlen(_msf_refGenName);
-
-					tmp = fwrite(&rNo, sizeof(int), 1, out1);
-
-					tmp = fwrite(&l, sizeof(char), 1, out1);
-					tmp = fwrite(_msf_refGenName, sizeof(char), l, out1);
-
-					tmp = fwrite(&loc, sizeof(int), 1, out1);
-					tmp = fwrite(&err, sizeof(int), 1, out1);
-					tmp = fwrite(&sc, sizeof(float), 1, out1);
-					
-					if(mi1[j].cigarSize > SEQ_LENGTH || mi1[j].cigarSize <= 0 )
-						printf("ERROR %d %s\n", mi1[j].cigarSize, _msf_seqList[i*2+1].seq);
-					
-					tmp = fwrite (&(mi1[j].cigarSize), sizeof(int), 1, out1);
-					tmp = fwrite ((mi1[j].cigar), sizeof(char), mi1[j].cigarSize, out1);
-
-					tmp = fwrite (&(mi1[j].mdSize), sizeof(int), 1, out1);
-					tmp = fwrite ((mi1[j].md), sizeof(char), mi1[j].mdSize, out1);
-					
-					_msf_oeaMapping[i*2]++;
-				}
-			}
-		}
-		
-		char *seq1, *seq2, *rseq1, *rseq2, *qual1, *qual2;
-
-
-
-		
-		rqual1[SEQ_LENGTH] = '\0'; 
-		rqual2[SEQ_LENGTH] = '\0';
-		rqual1[0] = '\0';
-		rqual2[0] = '\0';
-		
-
-
-		seq1 = _msf_seqList[i*2].seq;
-		rseq1 = _msf_seqList[i*2].rseq;
-		qual1 = _msf_seqList[i*2].qual;
-
-
-
-		strncpy(rqual1, _msf_seqList[i*2].qual, SEQ_LENGTH);
-		
-		seq2 = _msf_seqList[i*2+1].seq;
-		rseq2 = _msf_seqList[i*2+1].rseq;
-		qual2 = _msf_seqList[i*2+1].qual;
-		
-
-		strncpy(rqual2, _msf_seqList[i*2+1].qual, SEQ_LENGTH);
-		
-		if (pairedEndDiscordantMode)
-		{
-			for (k=0; k<size1; k++)
-			{
-				mi1[k].score = calculateScore(mi1[k].loc, (mi1[k].dir==-1)?rseq1:seq1, (mi1[k].dir==-1)?rqual1:qual1, mi1[k].cigar);
-			}
-
-			for (k=0; k<size2; k++)
-			{
-				mi2[k].score = calculateScore(mi2[k].loc, (mi2[k].dir==-1)?rseq2:seq2, (mi2[k].dir==-1)?rqual2:qual2, mi2[k].cigar);
-			}
-
-		}
-	
-
-		if (pairedEndDiscordantMode)
-		{
-			for (j=0; j<size1; j++)
-			{
-				for(k = 0; k < size2; k++)
-				{
-					if(
-							(mi2[k].loc-mi1[j].loc >= minPairEndedDiscordantDistance && 
-							 mi2[k].loc-mi1[j].loc <= maxPairEndedDiscordantDistance && 
-							 mi1[j].dir > 0 && mi2[k].dir < 0 ) 
-
-							|| 
-
-							(mi1[j].loc-mi2[k].loc >= minPairEndedDiscordantDistance &&
-							 mi1[j].loc-mi2[k].loc <= maxPairEndedDiscordantDistance &&
-							 mi1[j].dir < 0 && mi2[k].dir > 0)   
-					  )
-					{
-						//POSSIBLE CONCORDANT
-						if(_msf_readHasConcordantMapping[i] == 0)
-						{
-							setPairFullMappingInfo(i, mi1[j], mi2[k]);
-							_msf_readHasConcordantMapping[i] = 1;
-							_msf_seqList[i*2].hits[0] = 1;
-							_msf_seqList[i*2+1].hits[0] = 1;
-						}
-						else
-						{
-							if(bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err >= mi1[j].err + mi2[k].err)
-							{
-
-								if( bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err == 
-										mi1[j].err + mi2[k].err &&
-										findNearest(abs(bestHitMappingInfo[i*2+1].loc - bestHitMappingInfo[i*2].loc),
-											abs(mi2[k].loc - mi1[j].loc),
-											meanDistanceMapping	
-											) == 0 )
-								{
-									continue;
-								}
-								setPairFullMappingInfo(i, mi1[j], mi2[k]);
-							}
-						}	
-					}
-					//DISCORDANT TO TEMP FILE FOR POST PROCESSIING
-					else if(_msf_readHasConcordantMapping[i] == 0 && 
-						   	_msf_seqHits[i*2] != 0 && 
-							_msf_seqHits[i*2+1] != 0) 
-					{
-
-						int tmp;
-						int rNo = i;
-						int loc = mi1[j].loc*mi1[j].dir;
-						int err = mi1[j].err;
-						float sc = mi1[j].score;
-
-						char l = strlen(_msf_refGenName);
-
-						if(_msf_discordantMapping[i*2] < maxDiscordantOutput)
-						{
-							
-							tmp = fwrite(&rNo, sizeof(int), 1, out);
-
-							tmp = fwrite(&l, sizeof(char), 1, out);
-							tmp = fwrite(_msf_refGenName, sizeof(char), l, out);
-
-							tmp = fwrite(&loc, sizeof(int), 1, out);
-							tmp = fwrite(&err, sizeof(int), 1, out);
-							tmp = fwrite(&sc, sizeof(float), 1, out);
-
-							tmp = fwrite (&(mi1[j].cigarSize), sizeof(int), 1, out);
-							tmp = fwrite ((mi1[j].cigar), sizeof(char), mi1[j].cigarSize, out);
-
-							tmp = fwrite (&(mi1[j].mdSize), sizeof(int), 1, out);
-							tmp = fwrite ((mi1[j].md), sizeof(char), mi1[j].mdSize, out);
-
-
-							loc = mi2[k].loc*mi2[k].dir;
-							err = mi2[k].err;
-							sc = mi2[k].score;
-
-							tmp = fwrite(&loc, sizeof(int), 1, out);
-							tmp = fwrite(&err, sizeof(int), 1, out);
-							tmp = fwrite(&sc, sizeof(float), 1, out);
-
-							tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out);
-							tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out);
-
-							tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out);
-							tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out);
-
-							
-							_msf_discordantMapping[i*2]++;
-						}
-						//SET THE BEST DISCORDANT
-						//BEGIN {Farhad Hormozdiari}
-						if( bestHitMappingInfo[i*2].loc == -1 && 
-								bestHitMappingInfo[i*2+1].loc == -1 && 
-								_msf_readHasConcordantMapping[i] == 0)
-						{
-							setPairFullMappingInfo(i, mi1[j], mi2[k]);
-							_msf_seqList[i*2].hits[0] = 1;
-							_msf_seqList[i*2+1].hits[0] = 1;
-						}
-						else if( bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err >= mi1[j].err + mi2[k].err 
-								&&  _msf_readHasConcordantMapping[i] == 0)
-						{
-							if(bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err == mi1[j].err + mi2[k].err &&
-									findNearest( abs(bestHitMappingInfo[i*2+1].loc - bestHitMappingInfo[i*2].loc),
-										abs(mi1[j].loc - mi2[k].loc),
-										meanDistanceMapping
-										) == 0
-							  )
-							{
-								continue;
-							}
-							setPairFullMappingInfo(i, mi1[j], mi2[k]);	
-						}						
-						//END {Farhad Hormozdiari}
-					}
-				}
-			}
-		}
-		else
-		{
-			for (j=0; j<size1; j++)
-			{
-				for(k = 0; k < size2; k++)
-				{
-				  if((mi2[k].loc-mi1[j].loc >= minPairEndedDistance && 
-				      mi2[k].loc-mi1[j].loc <= maxPairEndedDistance && 
-				      mi1[j].dir > 0 && mi2[k].dir < 0)
-				     ||
-				     (mi1[j].loc-mi2[k].loc >= minPairEndedDistance &&
-				      mi1[j].loc-mi2[k].loc <= maxPairEndedDistance &&
-				      mi1[j].dir < 0 && mi2[k].dir > 0)
-					   )
-					{
-						char *seq;
-						char *qual;
-						char d1;
-						char d2;
-						int isize;
-						int proper=0;
-						// ISIZE CALCULATION
-						// The distance between outer edges								
-						isize = abs(mi1[j].loc - mi2[k].loc)+SEQ_LENGTH-2;	
-						if (mi1[j].loc - mi2[k].loc > 0)
-						{
-							isize *= -1;
-						}
-
-						d1 = (mi1[j].dir == -1)?1:0;
-						d2 = (mi2[k].dir == -1)?1:0;
-
-						//SET THE READ HAS CONCORDANT MAPPING
-						_msf_readHasConcordantMapping[i] = 1;
-
-						if ( d1 )
-						{
-							seq = rseq1;
-							qual = rqual1;
-						}
-						else
-						{
-							seq = seq1;
-							qual = qual1;
-						}
-
-						if ((mi1[j].loc < mi2[k].loc && !d1 && d2) ||
-						    (mi1[j].loc > mi2[k].loc && d1 && !d2) )
-						{
-							proper = 2;
-						}
-						else
-						{
-							proper = 0;
-						}
-
-	   
-						_msf_output.POS			= mi1[j].loc;
-						_msf_output.MPOS		= mi2[k].loc;
-						_msf_output.FLAG		= 1+proper+16*d1+32*d2+64;
-						_msf_output.ISIZE		= isize;
-						_msf_output.SEQ			= seq,
-						_msf_output.QUAL		= qual;
-						_msf_output.QNAME		= _msf_seqList[i*2].name;
-						_msf_output.RNAME		= _msf_refGenName;
-						_msf_output.MAPQ		= 255;
-						_msf_output.CIGAR		= cigar;
-						_msf_output.MRNAME		= "=";
-
-						_msf_output.optSize	= 2;
-						_msf_output.optFields	= _msf_optionalFields;
-
-						_msf_optionalFields[0].tag = "NM";
-						_msf_optionalFields[0].type = 'i';
-						_msf_optionalFields[0].iVal = mi1[j].err;
-
-						_msf_optionalFields[1].tag = "MD";
-						_msf_optionalFields[1].type = 'Z';
-						_msf_optionalFields[1].sVal = mi1[j].md;
-
-						if(!bestMode)
-							output(_msf_output);
-
-						if ( d2 )
-						{
-							seq = rseq2;
-							qual = rqual2;
-						}
-						else
-						{
-							seq = seq2;
-							qual = qual2;
-						}
-
-						_msf_output.POS			= mi2[k].loc;
-						_msf_output.MPOS		= mi1[j].loc;
-						_msf_output.FLAG		= 1+proper+16*d2+32*d1+128;
-						_msf_output.ISIZE		= -isize;
-						_msf_output.SEQ			= seq,
-						_msf_output.QUAL		= qual;
-						_msf_output.QNAME		= _msf_seqList[i*2].name;
-						_msf_output.RNAME		= _msf_refGenName;
-						_msf_output.MAPQ		= 255;
-						_msf_output.CIGAR		= cigar;
-						_msf_output.MRNAME		= "=";
-
-						_msf_output.optSize	= 2;
-						_msf_output.optFields	= _msf_optionalFields;
-
-						_msf_optionalFields[0].tag = "NM";
-						_msf_optionalFields[0].type = 'i';
-						_msf_optionalFields[0].iVal = mi2[k].err;;
-
-						_msf_optionalFields[1].tag = "MD";
-						_msf_optionalFields[1].type = 'Z';
-						_msf_optionalFields[1].sVal = mi2[k].md;
-
-						if(!bestMode)
-							output(_msf_output);	
-						//SET THE BEST CONCORDANT
-						//BEGIN {Farhad Hormozdiari}
-							if(bestHitMappingInfo[i*2].loc == -1 && bestHitMappingInfo[i*2+1].loc == -1)
-							{
-								setPairFullMappingInfo(i, mi1[j], mi2[k]);
-							}
-							else
-							{
-								if(bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err >= mi1[j].err + mi2[k].err)
-								{
-									
-									if( bestHitMappingInfo[i*2].err + bestHitMappingInfo[i*2+1].err == mi1[j].err + mi2[k].err &&
-									    findNearest(abs(bestHitMappingInfo[i*2+1].loc - bestHitMappingInfo[i*2].loc),
-										      abs(mi2[k].loc - mi1[j].loc),
-										      meanDistanceMapping	
-									    ) == 0 )
-									{
-										continue;
-									}
-									setPairFullMappingInfo(i, mi1[j], mi2[k]);
-								}
-							}		
-					//END   {Farhad Hormozdiari}
-					}
-				}
-			}		
-			
-		}
-	}
-
-	freeMem(rqual1, 0);
-	freeMem(rqual2, 0);
-	
-	if (pairedEndDiscordantMode)
-	{
-		fclose(out);
-		fclose(out1);
-	}
-
-	for (i=0; i<_msf_openFiles; i++)
-	{
-		fclose(in1[i]);
-		fclose(in2[i]);
-
-		unlink(fname1[i]);
-		unlink(fname2[i]);
-	}
-	
-	freeMem(mi1, sizeof(FullMappingInfo)*_msf_maxLSize);
-	freeMem(mi2, sizeof(FullMappingInfo)*_msf_maxRSize);
-
-	_msf_openFiles = 0;
-}
-
-/**********************************************/
-/**********************************************/
-/**********************************************/
-/**********************************************/
-float str2int(char *str, int index1, int index2)
-{
-	char tmp[200];
-	strncpy(tmp, &str[index1], index2-index1);
-	tmp[index2-index1] = '\0';
-	return atol(tmp);
-}
-
-float calculateScore(int index, char *seq, char *qual,char *md)
-{
-	int i;
-	int j;
-	char *ref;
-	char *ver;
-
-	ref = _msf_refGen + index-1;
-	ver = seq;
-	float score = 1;
-
-	char tmp[200];
-	int value = 0;
-	int end = 0;
-	int index1 = 0;
-	int index2 = 0;
-
-	i=0;
-	while(1)
-	{
-
-		if(i>=strlen(md))
-			break;
-		
-		index1 = i;
-
-		while(md[i] >='0' && md[i]<='9')
-		{
-			i++;
-		}
-		
-		index2 = i;
-
-		value = str2int(md, index1,index2);
-
-		if(md[i]=='M')
-		{
-			for(j=0;j<value;j++)
-			{
-				tmp[end]='M';
-				end++;
-			}
-		}
-		else if(md[i]=='I')
-		{
-			for(j=0;j<value;j++)
-			{
-				tmp[end]='I';
-				end++;
-			}
-
-		}
-		else if(md[i] == 'D')
-		{
-			for(j=0;j<value;j++)
-			{
-				tmp[end]='D';
-				end++;
-			}	
-		}	
-		i++;
-	}
-
-	tmp[end] = '\0';
-
-	j =  0;
-
-	for (i = 0; i < end; i++)
-	{
-		if(tmp[i] == 'M')	
-		{
-			if (*ref != *ver)
-			{
-				score *= 0.001 + 1/pow( 10, ((qual[j]-33)/10.0) );
-			}
-		
-			ref++;
-			ver++;
-			j++;
-		}
-		else if(tmp[i] == 'I')
-		{
-			ver++;
-			j++;
-		}
-		else if(tmp[i] == 'D') 
-		{
-			ref++;
-		}
-	}
-
-	return score;
-}
-
-int matoi(char *str, int start, int end)
-{
-	int i = 0;
-	char tmp[200];
-	
-	for(i=0;i < end-start; i++)
-		tmp[i] = str[start+i];
-	tmp[i]='\0';
-
-	return atoi(tmp);
-}
-
-void convertCigarToMatrix(char *cigar, int cigar_size, char * matrix)
-{
-	int i = 0;
-	int j = 0;	
-
-	int start = 0;
-	int size = 0;
-
-    matrix[0] = '\0';
-
-	while(i < cigar_size)
-	{
-		if(cigar[i] >= '0' && cigar[i] <= '9')
-		{	
-			start = i;
-
-			while(cigar[i] >= '0' && cigar[i] <= '9' && i < cigar_size)
-				i++;					
-
-			int value = matoi(cigar, start, i);
-			for(j = 0;  j < value; j++)
-			{
-				if(cigar[i] == 'M')
-					matrix[size] = 'M';
-				else if(cigar[i] == 'D')
-					matrix[size] ='D';
-				else if(cigar[i] == 'I')
-					matrix[size] = 'I';
-				size++;
-			}
-		}
-		i++;
-	}
-	matrix[size] = '\0';
-}
-
-
-
-void convertMDToMatrix(char *md, int md_size, char * matrix)
-{
-	int i = 0;
-	int j = 0;	
-
-	int start = 0;
-	int size = 0;
-
-    matrix[0] = '\0';
-
-	while(i < md_size)
-	{
-		if(md[i] >= '0' && md[i] <= '9')
-		{	
-			start = i;
-
-			while(md[i] >= '0' && md[i] <= '9' && i < md_size)
-				i++;					
-
-			int value = matoi(md, start, i);
-			for(j = 0;  j < value; j++)
-			{
-				matrix[size] = 'M';	
-				size++;
-			}
-			i--;
-		}
-		else if(md[i] == '^')
-		{
-			matrix[size] = 'D';	
-			size++;
-		}
-		else
-		{
-			 matrix[size] = md[i];
-             size++;		 
-		}
-		//size++;
-		i++;
-	}
-	matrix[size] = '\0';
-}
-
-
-void convertMDCigarToMatrix(char *cigar, int cigar_size, char *md, int md_size, char *matrix)
-{
-	int i = 0;
-	int j = 0;
-	
-	int size = 0;
-	
-	char tmp1[200];
-	char tmp2[200];
-	convertMDToMatrix(md,md_size, tmp2);
-
-	convertCigarToMatrix(cigar, cigar_size,tmp1);
-
-	
-	
-	while(i < strlen(tmp1))
-	{
-		if(tmp1[i]=='M')
-		{
-			if(j < strlen(tmp2))
-			{
-				if(tmp2[j]=='M')
-				{
-					matrix[size]='M';
-					size++;
-				}
-				if(tmp2[j]!='M')
-				{
-					matrix[size]=tmp2[j];
-					size++;
-				}
-			}
-			else
-			{
-				matrix[size]='M';
-				size++;
-			}
-		}
-		else if(tmp1[i] == 'D')
-		{
-			matrix[size]='D';
-			size++;
-			j++;
-			matrix[size]=tmp2[j];
-			size++;
-			
-		}
-		else if(tmp1[i] == 'I')
-		{
-			matrix[size]='I';
-			size++;
-		}
-		
-		i++;
-		if(j < strlen(tmp2))
-			j++;
-	}
-	
-	if(strlen(tmp1))
-	
-	matrix[size] = '\0';
-
-}
-
-void convertInsertion(char * in_matrix, char * seq, char *out_matrix)
-{
-	int i = 0;
-	int j = 0;
-	int size = 0;
-	
-	while( i  < strlen(in_matrix))
-	{
-		if(in_matrix[i] == 'M')
-		{
-			out_matrix[size] = 'M';
-			size++;
-			j++;
-		}
-		else if(in_matrix[i] == 'D')
-		{
-			out_matrix[size] = 'D';
-			size++;
-
-			i++;
-			j++;
-
-			out_matrix[size] = seq[j];
-			j++;
-			size++;
-		}
-		else if(in_matrix[i] == 'I')
-		{
-			out_matrix[size] = 'I';
-			size++;
-			out_matrix[size] = seq[j];
-			size++;
-			j++;
-		}
-		else
-		{
-			out_matrix[size] = in_matrix[i];
-			size++;
-			j++;
-		}
-		i++;
-	}
-	out_matrix[size] = '\0';
-}
-
-/**********************************************/
-void outputPairedEndDiscPP()
-{
-	char tmp_matrix1[200];
-	char tmp_matrix2[200];
-
-	char matrix1[200];
-	char matrix2[200];
-
-	char cigar1[200];
-	char editString1[200];
-
-	char cigar2[200];
-	char editString2[200];
-	
-	char seq1[SEQ_LENGTH+1];
-	char qual1[SEQ_LENGTH+1];
-    
-	char seq2[SEQ_LENGTH+1];
-	char qual2[SEQ_LENGTH+1];
-   	
-	char genName[SEQ_LENGTH];
-	char fname1[FILE_NAME_LENGTH];
-	char fname2[FILE_NAME_LENGTH];
-	char l;
-	int l_size;
-	int loc1, loc2;
-	int err1, err2;
-	char dir1, dir2;
-	float sc1, sc2, lsc=0;
-	int flag = 0;
-	int rNo,lrNo = -1;
-	int tmp;
-	FILE *in, *out;
-
-	sprintf(fname1, "%s__%s__disc", mappingOutputPath, mappingOutput);
-	sprintf(fname2, "%s%s_DIVET.vh", mappingOutputPath, mappingOutput);
-
-	in   = fileOpen(fname1, "r");
-	out  = fileOpen(fname2, "w");
-	
-	if (in != NULL)
-	{
-		flag = fread(&rNo, sizeof(int), 1, in);
-	}
-	else
-	{
-		flag  = 0;
-	}
-
-	seq1[SEQ_LENGTH]   = '\0';
-	qual1[SEQ_LENGTH]  = '\0';
-
-	seq2[SEQ_LENGTH]   = '\0';
-	qual2[SEQ_LENGTH]  = '\0';
-
-	while (flag)
-	{
-		tmp = fread(&l, sizeof(char), 1, in);
-		tmp = fread(genName, sizeof(char), l, in);
-		genName[(int)l]='\0';
-		tmp = fread(&loc1, sizeof(int), 1, in);
-		tmp = fread(&err1, sizeof(int), 1, in);
-		tmp = fread(&sc1, sizeof(float), 1, in);
-
-		//tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out);
-		
-		tmp = fread(&l_size, sizeof(int), 1, in);
-		tmp = fread(cigar1, sizeof(char), l_size, in);
-		cigar1[(int)l_size]='\0';
-		//tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out);
-
-		//tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out);
-		tmp = fread(&l_size, sizeof(int), 1, in);
-		tmp = fread(editString1, sizeof(char), l_size, in);
-		editString1[(int)l_size]='\0';
-		//tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out);
-
-		tmp = fread(&loc2, sizeof(int), 1, in);
-		tmp = fread(&err2, sizeof(int), 1, in);
-		tmp = fread(&sc2, sizeof(float), 1, in);
-
-		tmp = fread(&l_size, sizeof(int), 1, in);
-		tmp = fread(cigar2, sizeof(char), l_size, in);
-		cigar2[(int)l_size]='\0';
-
-		tmp = fread(&l_size, sizeof(int), 1, in);
-		tmp = fread(editString2, sizeof(char), l_size, in);
-		editString2[(int)l_size]='\0';
-	
-		convertMDCigarToMatrix(cigar1, strlen(cigar1), editString1, strlen(editString1), tmp_matrix1);
-		convertMDCigarToMatrix(cigar2, strlen(cigar2), editString2, strlen(editString2), tmp_matrix2);
-	
-		
-		if(_msf_readHasConcordantMapping[rNo] == 0)
-		{
-			
-			dir1 = dir2 = 'F';
-
-			strncpy(seq1, _msf_seqList[rNo*2].seq, SEQ_LENGTH);
-			strncpy(seq2, _msf_seqList[rNo*2+1].seq, SEQ_LENGTH);
-
-			if (loc1 < 0)
-			{
-				dir1 = 'R';
-				loc1 = -loc1;
-
-				strncpy(seq1, _msf_seqList[rNo*2].rseq, SEQ_LENGTH);
-			}
-
-			if (loc2 < 0)
-			{
-				dir2 = 'R';
-				loc2 = -loc2;
-
-				strncpy(seq2, _msf_seqList[rNo*2+1].rseq, SEQ_LENGTH);
-			}
-	
-			convertInsertion(tmp_matrix1, seq1, matrix1);
-			convertInsertion(tmp_matrix2, seq2, matrix2);
-		
-			
-			if (rNo != lrNo)
-			{
-				int j;
-				for (j=0; j<SEQ_LENGTH; j++)
-				{
-					lsc += _msf_seqList[rNo*2].qual[j]+_msf_seqList[rNo*2+1].qual[j];
-				}
-				lsc /= 2*SEQ_LENGTH;
-				lsc -= 33;
-				lrNo = rNo;
-			}
-
-			char event = '\0';
-
-
-			if ( dir1 == dir2 )
-			{
-				event = 'V';
-			}
-			else
-			{
-				if (loc1 < loc2)
-				{
-
-					if (dir1 == 'R' && dir2 == 'F')
-					{
-						event = 'E';
-
-					}
-					else if ( loc2 - loc1 >= maxPairEndedDiscordantDistance )
-					{
-						event = 'D';
-					}
-					else
-					{
-						event = 'I';
-					}
-				}
-				else if (loc2 < loc1)
-				{
-					if (dir2 == 'R' && dir1 == 'F')
-					{
-						event = 'E';
-					}
-					else if ( loc1 - loc2 >= maxPairEndedDiscordantDistance )
-					{
-						event = 'D';
-					}
-					else
-					{
-						event = 'I';
-					}
-				}
-			}
-			_msf_seqList[rNo*2].hits[0] = 2;
-			if(event != 'E')
-				fprintf(out, "%s\t%s\t%d\t%d\t%c\t%d\t%d\t%c\t%c\t%d\t%0.0f\t%e\n",
-					_msf_seqList[rNo*2].name, genName, loc1, (loc1+SEQ_LENGTH-1), dir1, 
-					loc2, (loc2+SEQ_LENGTH-1), dir2, event, (err1+err2), lsc, sc1*sc2);			
-
-		}
-		flag = fread(&rNo, sizeof(int), 1, in);
-	}
-
-	fclose(in);
-	fclose(out);
-
-	unlink(fname1);
-}
-
-void finalizeOEAReads(char *fileName)
-{
-	FILE *fp_out1;
-	FILE * in;
-		
-	char genName[SEQ_LENGTH];
-	
-	char fname1[FILE_NAME_LENGTH];
-	char fname2[FILE_NAME_LENGTH];
-	
-	char l=0;
-	int loc1=0;
-	
-	int err1;
-
-	char d;
-	
-	float sc1=0;
-	int flag = 0;
-	int rNo=-1;
-	int tmp=0;
-	
-	int cigarSize = 0;
-	int mdSize = 0;
-	
-	char cigar[SEQ_LENGTH+1];
-	char md[SEQ_LENGTH+1];
-
-	char *seq1, *seq2, *qual1, *qual2;
-	char *rqual1, *rqual2;
-	
-	seq1=NULL; seq2=NULL; qual1=NULL; qual2=NULL;
-
-	rqual1 = getMem(200*sizeof(char));
-	rqual2 = getMem(200*sizeof(char));
-	
-	rqual1[0] = '\0';
-	rqual2[0] = '\0';
-
-	sprintf(fname1, "%s%s_OEA", mappingOutputPath, mappingOutput);
-
-	fp_out1 = fileOpen(fname1, "w");
-
-	in = NULL;
-	if (pairedEndDiscordantMode){
-	  sprintf(fname2, "%s__%s__oea", mappingOutputPath, mappingOutput);
-	  
-	  in   = fileOpen(fname2, "r");
-	}
-
-
-	if (in != NULL)
-	{
-		flag = fread(&rNo, sizeof(int), 1, in);
-	}
-	else
-	{
-		flag  = 0;
-	}
-
-	while (flag)
-	{
-		cigar[0] = '\0';
-		md[0] = '\0';
-
-		tmp = fread(&l, sizeof(char), 1, in);
-		tmp = fread(genName, sizeof(char), l, in);
-	
-		genName[(int)l]='\0';
-	
-		
-		tmp = fread(&loc1, sizeof(int), 1, in);
-		tmp = fread(&err1, sizeof(int), 1, in);
-		tmp = fread(&sc1, sizeof(float), 1, in);
-		
-		tmp = fread (&cigarSize, sizeof(int), 1, in);
-		tmp = fread (cigar, sizeof(char), cigarSize, in);
-
-		cigar[cigarSize] = '\0';
-		
-		tmp = fread (&mdSize, sizeof(int), 1, in);
-		tmp = fread (md, sizeof(char), mdSize, in);
-		md[mdSize] = '\0';
-		
-		d = 1;
-		
-		if(loc1 < 0)
-		{
-			d = -1;
-			loc1 *= -1;
-			
-			seq1 = _msf_seqList[rNo].rseq;
-			reverse(_msf_seqList[rNo].qual, rqual1, SEQ_LENGTH);
-			rqual1[SEQ_LENGTH] = '\0';
-		}
-		else
-		{
-			seq1 = _msf_seqList[rNo].seq;
-			qual1 = _msf_seqList[rNo].qual;
-		}
-
-		if(rNo % 2 == 0)
-		{
-			seq2 = _msf_seqList[rNo+1].seq;
-			qual2 = _msf_seqList[rNo+1].qual;
-		}
-		else 
-		{
-			seq2 = _msf_seqList[rNo-1].seq;
-			qual2 = _msf_seqList[rNo-1].qual;
-		}
-		
-		if(_msf_seqHits[rNo] != 0 && _msf_seqHits[(rNo%2==0)?rNo+1:rNo-1] == 0)
-		{	
-			_msf_output.POS                 = loc1;
-			_msf_output.MPOS                = 0;
-			_msf_output.FLAG                = (rNo % 2 ==0)? 1+4+32*d+128  : 1+8+16*d+64 ;
-			_msf_output.ISIZE               = 0;
-			_msf_output.SEQ                 = seq1;
-			_msf_output.QUAL                = qual1;
-			_msf_output.QNAME               = _msf_seqList[rNo].name;
-			_msf_output.RNAME               = genName;
-			_msf_output.MAPQ                = 255;
-			_msf_output.CIGAR               = cigar;
-			_msf_output.MRNAME              = "=";
-
-
-			_msf_output.optSize     = 4;
-			_msf_output.optFields   = _msf_optionalFields;
-
-			_msf_optionalFields[0].tag = "NM";
-			_msf_optionalFields[0].type = 'i';
-			_msf_optionalFields[0].iVal = err1;
-
-			_msf_optionalFields[1].tag = "MD";
-			_msf_optionalFields[1].type = 'Z';
-			_msf_optionalFields[1].sVal = md;
-
-
-
-			//for the OEA reads
-			_msf_optionalFields[2].tag = "NS";
-			_msf_optionalFields[2].type = 'Z';
-			_msf_optionalFields[2].sVal = seq2;
-
-
-			_msf_optionalFields[3].tag = "NQ";
-			_msf_optionalFields[3].type = 'Z';
-			_msf_optionalFields[3].sVal = qual2;
-
-			outputSAM(fp_out1, _msf_output);
-
-			_msf_seqList[rNo].hits[0] = -1;
-			_msf_seqList[(rNo%2==0)?rNo+1:rNo-1].hits[0] = -1;
-		}
-		flag = fread(&rNo, sizeof(int), 1, in);
-	}
-
-	freeMem(rqual1, 0);
-	freeMem(rqual2, 0);
-
-	unlink(fname2);
-	
-	fclose(fp_out1);
-}
-
-/*
-
-void outputOEA(char *fileName1, FILE * fp_out, int readSegment)
-{
-	int i = 0; 
-	int j = 0;
-	
-	char *index;
-
-	int size1 = 0;
-
-	FILE *fp1;
-
-	char geneFileName1[FILE_NAME_LENGTH];
-
-	char matrix[200];
-	char cigar[MAX_CIGAR_SIZE];
-	char editString[200];
-
-	FullMappingInfoLink *miL = getMem(_msf_seqListSize * sizeof(FullMappingInfoLink));
-
-	if(fileName1 != NULL)
-	{
-
-		fp1 = fileOpen(fileName1, "r");
-		
-		index = strstr(fileName1, "__");
-		strncpy(geneFileName1, index + 2 * sizeof(char), strstr(index + 2, "__") - index - 2);
-		geneFileName1[strstr(index + 2, "__") - index - 2] = '\0';
-
-		for(i = 0; i < _msf_seqListSize / 2; i++)
-		{
-			fread(&size1, sizeof(int), 1, fp1);
-
-			miL[i].mi = getMem(size1 * sizeof(FullMappingInfo) );
-
-			miL[i].size = size1;
-
-			for(j = 0; j < size1; j++)
-			{
-				fread(&(miL[i].mi[j].loc), sizeof(int), 1, fp1);
-
-				fread (&(miL[i].mi[j].err), sizeof(int), 1, fp1);
-
-				fread (&(miL[i].mi[j].cigarSize), sizeof(int), 1, fp1);
-				fread ((miL[i].mi[j].cigar), sizeof(char), miL[i].mi[j].cigarSize+1, fp1);
-
-				fread (&(miL[i].mi[j].mdSize), sizeof(int), 1, fp1);
-				fread ((miL[i].mi[j].md), sizeof(char), miL[i].mi[j].mdSize+1, fp1);
-
-				miL[i].mi[j].dir = 1;
-				if(miL[i].mi[j].loc < 1) 
-				{
-					miL[i].mi[j].loc *= -1;
-					miL[i].mi[j].dir = -1;
-				}
-			}
-			
-			int tmpSize = (readSegment==0) ? _msf_seqHits[i*2+1]  : _msf_seqHits[i*2];
-			
-			if(_msf_seqHits[i*2+readSegment] == 0 && size1 != 0 && _msf_oeaMapping[i*2+(readSegment == 0 ? 1: 0)] <= maxOEAOutput)
-			{	
-				int d1 = 0;
-		
-				char *seq, *qual;
-				char *seq1, *seq2, *rseq1, *rseq2, *qual1, *qual2;
-				char rqual1[SEQ_LENGTH+1], rqual2[SEQ_LENGTH+1];
-				
-				rqual1[SEQ_LENGTH] = rqual2[SEQ_LENGTH] = '\0';
-				seq1 = _msf_seqList[i*2].seq;
-				rseq1 = _msf_seqList[i*2].rseq;
-				qual1 = _msf_seqList[i*2].qual;
-				reverse(_msf_seqList[i*2].qual, rqual1, SEQ_LENGTH);
-
-				seq2 = _msf_seqList[i*2+1].seq;
-				rseq2 = _msf_seqList[i*2+1].rseq;
-				qual2 = _msf_seqList[i*2+1].qual;
-				reverse(_msf_seqList[i*2+1].qual, rqual2, SEQ_LENGTH);
-
-				for(j = 0; j < size1 && _msf_oeaMapping[i*2+(readSegment == 0 ? 1: 0)] <= maxOEAOutput; j++)
-				{
-					d1 = (miL[i].mi[j].dir == -1)?1:0;
-
-					if(readSegment == 0)
-					{
-						if ( d1 )
-						{
-							seq = rseq2;
-							qual = rqual2;
-						}
-						else
-						{
-							seq = seq2;
-							qual = qual2;
-						}
-					}
-					else
-					{
-						if ( d1 )
-						{
-							seq = rseq1;
-							qual = rqual1;
-						}
-						else
-						{
-							seq = seq1;
-							qual = qual1;
-						}
-					}
-
-					_msf_oeaMapping[i*2+(readSegment == 0 ? 1: 0)]++;
-
-					_msf_output.POS                 = (readSegment==1)?miL[i].mi[j].loc:0;
-					_msf_output.MPOS                = (readSegment==0)?miL[i].mi[j].loc:0;
-					_msf_output.FLAG                = (readSegment==0)? 1+4+32*d1+128  : 1+8+16*d1+64 ;
-					_msf_output.ISIZE               = 0;
-					_msf_output.SEQ                 = seq,
-					_msf_output.QUAL                = qual;
-					_msf_output.QNAME               = _msf_seqList[i*2+(readSegment==0?1:0)].name;
-					_msf_output.RNAME               = geneFileName1;
-					_msf_output.MAPQ                = 255;
-					_msf_output.CIGAR               = miL[i].mi[j].cigar;
-					_msf_output.MRNAME              = "=";
-					//_msf_output.NSEQ                = (readSegment == 0)?seq1:seq2;
-					//_msf_output.NQUAL               = (readSegment == 0)?qual1:qual2;
-
-					
-					_msf_output.optSize     = 4;
-					_msf_output.optFields   = _msf_optionalFields;
-
-					_msf_optionalFields[0].tag = "NM";
-					_msf_optionalFields[0].type = 'i';
-					_msf_optionalFields[0].iVal = miL[i].mi[j].err;
-
-					_msf_optionalFields[1].tag = "MD";
-					_msf_optionalFields[1].type = 'Z';
-					_msf_optionalFields[1].sVal = miL[i].mi[j].md;
-
-
-
-					//for the OEA reads
-					_msf_optionalFields[2].tag = "NS";
-					_msf_optionalFields[2].type = 'Z';
-					_msf_optionalFields[2].sVal = (readSegment == 0)?seq1:seq2;
-
-
-					_msf_optionalFields[3].tag = "NQ";
-					_msf_optionalFields[3].type = 'Z';
-					_msf_optionalFields[3].sVal = (readSegment == 0)?qual1:qual2;
-
-					outputSAM(fp_out, _msf_output);
-							   
-				}
-			}
-		}
-		
-	}
-
-	for(i = 0; i < _msf_seqListSize / 2; i++)
-	{
-		freeMem(miL[i].mi, miL[i].size * sizeof(FullMappingInfo));
-	}
-	
-	freeMem(miL, _msf_seqListSize * sizeof(FullMappingInfoLink));
-
-	fclose(fp1);
-}
-
-void finalizeOEAReads(char *fileName)
-{
-
-	int i = 0;
-	int k = 0;
-
-	FILE *fp_out1;
-	char fname1[200];
-
-	_msf_oeaMapping = getMem(_msf_seqListSize * sizeof(int));
-	for(i = 0; i < _msf_seqListSize; i++)
-	{
-		_msf_oeaMapping[i] = 0;
-	}
-	
-	sprintf(fname1, "%s%s_OEA", mappingOutputPath, mappingOutput);
-
-	fp_out1 = fileOpen(fname1, "w");
-	for(i = 0; i < _msf_maxFile; i++)
-	{
-		for(k = 0; k < _msf_fileCount[i]; k++)
-		{
-			outputOEA(_msf_fileName[i][k][1], fp_out1, 0);
-		}// for k       
-	} //for i
-
-
-	for(i = 0; i < _msf_maxFile; i++)
-	{
-		for(k = 0; k < _msf_fileCount[i]; k++)
-		{
-			outputOEA(_msf_fileName[i][k][0], fp_out1, 1);
-		}// for k       
-	} //for i
-
-	fclose(fp_out1);
-
-}
-*/
-
-void outputTransChromosal(char *fileName1, char *fileName2, FILE * fp_out)
-{
-	int i = 0; 
-	int j = 0;
-	int k = 0;
-	
-	char *index;
-
-	int size1 = 0;
-	int size2 = 0;
-
-	FILE *fp1 = NULL;
-	FILE *fp2 = NULL;
-
-	char geneFileName1[FILE_NAME_LENGTH];
-	char geneFileName2[FILE_NAME_LENGTH];
-
-	FullMappingInfoLink *miL = getMem(_msf_seqListSize * sizeof(FullMappingInfoLink));
-	FullMappingInfoLink *miR = getMem(_msf_seqListSize * sizeof(FullMappingInfoLink));	
-
-
-	if(fileName1 != NULL && fileName2 != NULL)
-	{
-
-		fp1 = fileOpen(fileName1, "r");
-		fp2 = fileOpen(fileName2, "r");
-		
-		index = strstr(fileName1, "__");
-		strncpy(geneFileName1, index + 2 * sizeof(char), strstr(index + 2, "__") - index - 2);
-		geneFileName1[strstr(index + 2, "__") - index - 2] = '\0';
-
-                index = strstr(fileName2, "__");
-                strncpy(geneFileName2, index + 2 * sizeof(char), strstr(index + 2, "__") - index - 2);
-		geneFileName2[strstr(index + 2, "__") - index - 2] = '\0';
-
-
-		for(i = 0; i < _msf_seqListSize / 2; i++)
-		{
-			fread(&size1, sizeof(int), 1, fp1);
-			fread(&size2, sizeof(int), 1, fp2);
-
-			miL[i].mi = getMem(size1 * sizeof(FullMappingInfo) );
-			miR[i].mi = getMem(size2 * sizeof(FullMappingInfo) );
-
-			miL[i].size = size1;
-			miR[i].size = size2;
-
-			for(j = 0; j < size1; j++)
-			{
-				fread(&(miL[i].mi[j].loc), sizeof(int), 1, fp1);
-
-				fread (&(miL[i].mi[j].err), sizeof(int), 1, fp1);
-
-                                fread (&(miL[i].mi[j].cigarSize), sizeof(int), 1, fp1);
-                                fread ((miL[i].mi[j].cigar), sizeof(char), miL[i].mi[j].cigarSize+1, fp1);
-
-                                fread (&(miL[i].mi[j].mdSize), sizeof(int), 1, fp1);
-                                fread ((miL[i].mi[j].md), sizeof(char), miL[i].mi[j].mdSize+1, fp1);
-
-				miL[i].mi[j].dir = 1;
-				if(miL[i].mi[j].loc < 1) 
-				{
-					miL[i].mi[j].loc *= -1;
-  					miL[i].mi[j].dir = -1;
-				}
-			}
-			for(k = 0; k < size2; k++)
-			{
-                                fread(&(miR[i].mi[k].loc), sizeof(int), 1, fp2);
-
-				fread (&(miR[i].mi[k].err), sizeof(int), 1, fp2);
-
-                                fread (&(miR[i].mi[k].cigarSize), sizeof(int), 1, fp2);
-                                fread ((miR[i].mi[k].cigar), sizeof(char), miR[i].mi[k].cigarSize+1, fp2);
-
-                                fread (&(miR[i].mi[k].mdSize), sizeof(int), 1, fp2);
-                                fread ((miR[i].mi[k].md), sizeof(char), miR[i].mi[k].mdSize+1, fp2);
-
- 	 			miR[i].mi[k].dir = 1;
-                                if(miR[i].mi[k].loc < 1)
-                                {
-                                        miR[i].mi[k].loc *= -1;
-                                        miR[i].mi[k].dir = -1;
-                                }
-			}
-			if(_msf_readHasConcordantMapping[i] == 0 && size1 != 0 && size2 != 0 && (size1 * size2 < MAX_TRANS_CHROMOSAL_OUTPUT))
-			{	
-				int d1 = 0;
-				int d2 = 0;
-				char *seq, *qual;
-				char *seq1, *seq2, *rseq1, *rseq2, *qual1, *qual2;
-		                char rqual1[SEQ_LENGTH+1], rqual2[SEQ_LENGTH+1];
-		                rqual1[SEQ_LENGTH] = rqual2[SEQ_LENGTH] = '\0';
-			        seq1 = _msf_seqList[i*2].seq;
-		                rseq1 = _msf_seqList[i*2].rseq;
-			        qual1 = _msf_seqList[i*2].qual;
-		                reverse(_msf_seqList[i*2].qual, rqual1, SEQ_LENGTH);
-	
-        		        seq2 = _msf_seqList[i*2+1].seq;
-		                rseq2 = _msf_seqList[i*2+1].rseq;
-                		qual2 = _msf_seqList[i*2+1].qual;
-		                reverse(_msf_seqList[i*2+1].qual, rqual2, SEQ_LENGTH);
-
-				for(j = 0; j < size1; j++)
-				{
-					d1 = (miL[i].mi[j].dir == -1)?1:0;
-
-                                        if ( d1 )
-					{
-						seq = rseq1;
-						qual = rqual1;
-					}
-					else
-					{
-						seq = seq1;
-						qual = qual1;
-					}
-		
-					for(k = 0; k < size2; k++)
-					{
-	
-                	                        d2 = (miR[i].mi[k].dir == -1)?1:0;
-
-                                                _msf_output.POS                 = miL[i].mi[j].loc;
-                                                _msf_output.MPOS                = miR[i].mi[k].loc;
-                                                _msf_output.FLAG                = 0;
-                                                _msf_output.ISIZE               = 0;
-                                                _msf_output.SEQ                 = seq,
-                                                _msf_output.QUAL                = qual;
-                                                _msf_output.QNAME               = _msf_seqList[i*2].name;
-                                                _msf_output.RNAME               = geneFileName1;
-                                                _msf_output.MAPQ                = 255;
-                                                _msf_output.CIGAR               = miL[i].mi[j].cigar;
-                                                _msf_output.MRNAME              = "=";
-
-                                                _msf_output.optSize     = 2;
-                                                _msf_output.optFields   = _msf_optionalFields;
-
-                                                _msf_optionalFields[0].tag = "NM";
-                                                _msf_optionalFields[0].type = 'i';
-                                                _msf_optionalFields[0].iVal = miL[i].mi[j].err;
-
-                                                _msf_optionalFields[1].tag = "MD";
-                                                _msf_optionalFields[1].type = 'Z';
-                                                _msf_optionalFields[1].sVal = miL[i].mi[j].md;
-
-
-						if ( d2 )
-                                                {
-                                                        seq = rseq2;
-                                                        qual = rqual2;
-                                                }
-                                                else
-                                                {
-                                                        seq = seq2;
-                                                        qual = qual2;
-                                                }
-
-                                                outputSAM(fp_out, _msf_output);
-						
-
-       					 	_msf_output.POS                 = miR[i].mi[k].loc;
-                                                _msf_output.MPOS                = miL[i].mi[j].loc;
-                                                _msf_output.FLAG                = 0;
-                                                _msf_output.ISIZE               = 0;
-                                                _msf_output.SEQ                 = seq,
-                                                _msf_output.QUAL                = qual;
-                                                _msf_output.QNAME               = _msf_seqList[i*2+1].name;
-                                                _msf_output.RNAME               = geneFileName2;
-                                                _msf_output.MAPQ                = 255;
-                                                _msf_output.CIGAR               = miR[i].mi[k].cigar;
-                                                _msf_output.MRNAME              = "=";
-
-                                                _msf_output.optSize     = 2;
-                                                _msf_output.optFields   = _msf_optionalFields;
-						
-                                                _msf_optionalFields[0].tag = "NM";
-                                                _msf_optionalFields[0].type = 'i';
-                                                _msf_optionalFields[0].iVal = miR[i].mi[k].err;
-
-                                                _msf_optionalFields[1].tag = "MD";
-                                                _msf_optionalFields[1].type = 'Z';
-                                                _msf_optionalFields[1].sVal = miR[i].mi[k].md;
-
-                                                outputSAM(fp_out, _msf_output);
-
-					}							   
-				}
-			}
-		}
-		
-	}
-
-	for(i = 0; i < _msf_seqListSize / 2; i++)
-	{
-		freeMem(miL[i].mi, miL[i].size * sizeof(FullMappingInfo));
-		freeMem(miR[i].mi, miR[i].size * sizeof(FullMappingInfo));	
-	}
-	
-	freeMem(miL, _msf_seqListSize * sizeof(FullMappingInfoLink));
-        freeMem(miR, _msf_seqListSize * sizeof(FullMappingInfoLink));
-
-	fclose(fp1);
-	fclose(fp2);
-}
-
-/*
-	if flag is 1 it will output all the possible trans chromsal mapping
-	otherwise only tmp file will be delete
-	
-*/
-
-void outputAllTransChromosal(int flag)
-{
-	
-	int i = 0; 
-	int j = 0;
-	int k = 0;
-	int l = 0;
-
-	FILE *fp_out = NULL;
-	char fname1[200];
-
-	if(flag)
-	{
-	        fp_out = fileOpen(fname1, "w");
-
-	        sprintf(fname1, "%s%s_TRANSCHROMOSOMAL", mappingOutputPath, mappingOutput);
-
-	//	for(i = 0; i < _msf_maxFile; i++)
-	//	{
-			i  = 0;
-			for(j = i+1; j < _msf_maxFile; j++)
-			{
-				if(i != j) 
-				{
-					for(k = 0; k < _msf_fileCount[i]; k++) 
-					{
-						for(l = 0; l < _msf_fileCount[j]; l++) 
-						{
-							outputTransChromosal(_msf_fileName[i][k][0], _msf_fileName[j][l][1], fp_out);
-						}// for l
-					}// for k	
-				}// if
-			}// for j
-	//	} //for i		
-	}
-
-	for(i = 0; i < _msf_maxFile; i++)
-	{
-		for(j = 0; j < _msf_fileCount[i]; j++)
-		{
-			unlink(_msf_fileName[i][j][0]);
-			unlink(_msf_fileName[i][j][1]);
-		}
-	}	
-	if(flag)
-	  fclose(fp_out);
-}