--- a/mrfast-2.1.0.4/Reads.c	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,773 +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 <ctype.h>
-#include <zlib.h>
-#include "Common.h"
-#include "Reads.h"
-
-#define CHARCODE(a) (a=='A' ? 0 : (a=='C' ? 1 : (a=='G' ? 2 : (a=='T' ? 3 : 4))))
-
-FILE *_r_fp1;
-FILE *_r_fp2;
-gzFile _r_gzfp1;
-gzFile _r_gzfp2;
-Read *_r_seq;
-int _r_seqCnt;
-int *_r_samplingLocs;
-
-/**********************************************/
-char *(*readFirstSeq)(char *);
-char *(*readSecondSeq)(char *);
-/**********************************************/
-char *readFirstSeqTXT( char *seq )
-{
-	return fgets(seq, SEQ_MAX_LENGTH, _r_fp1);
-}
-
-/**********************************************/
-char *readSecondSeqTXT( char *seq )
-{
-	return fgets(seq, SEQ_MAX_LENGTH, _r_fp2);
-}
-/**********************************************/
-char *readFirstSeqGZ( char *seq )
-{
-	return gzgets(_r_gzfp1, seq, SEQ_MAX_LENGTH);
-}
-
-/**********************************************/
-char *readSecondSeqGZ( char *seq )
-{
-	return gzgets(_r_gzfp2, seq, SEQ_MAX_LENGTH);
-}
-/**********************************************/
-int toCompareRead(const void * elem1, const void * elem2)
-{
-	return strcmp(((Read *)elem1)->seq, ((Read *)elem2)->seq);	
-}
-/**********************************************/
-int readAllReads(char *fileName1,
-						char *fileName2,
-						int compressed,
-						unsigned char *fastq,
-						unsigned char pairedEnd,
-						Read **seqList,
-						unsigned int *seqListSize)
-{
-	double startTime=getTime();
-
-	char seq1[SEQ_MAX_LENGTH];
-	char rseq1[SEQ_MAX_LENGTH];
-	char name1[SEQ_MAX_LENGTH];
-	char qual1[SEQ_MAX_LENGTH];
-	char seq2[SEQ_MAX_LENGTH];
-	char rseq2[SEQ_MAX_LENGTH];
-	char name2[SEQ_MAX_LENGTH];
-	char qual2[SEQ_MAX_LENGTH];
-
-	char dummy[SEQ_MAX_LENGTH];
-	char ch;
-	int err1, err2;
-	int nCnt;
-	int discarded = 0;
-	int seqCnt = 0;
-	int maxCnt = 0;
-	int i;
-	Read *list = NULL;
-
-	int clipped = 0;
-
-	if (!compressed)
-	{
-		_r_fp1 = fileOpen( fileName1, "r");
-
-		if (_r_fp1 == NULL)
-		{
-			return 0;
-		}
-
-		ch = fgetc(_r_fp1);
-
-		if ( pairedEnd && fileName2 != NULL )
-		{
-			_r_fp2 = fileOpen ( fileName2, "r" );
-			if (_r_fp2 == NULL)
-			{
-				return 0;
-			}
-		}
-		else
-		{
-			_r_fp2 = _r_fp1;
-		}
-
-		readFirstSeq = &readFirstSeqTXT;
-		readSecondSeq = &readSecondSeqTXT;
-	}
-	else
-	{
-
-		_r_gzfp1 = fileOpenGZ (fileName1, "r");
-
-		if (_r_gzfp1 == NULL)
-		{
-			return 0;
-		}
-
-		ch = gzgetc(_r_gzfp1);
-
-		if ( pairedEnd && fileName2 != NULL )
-		{
-			_r_gzfp2 = fileOpenGZ ( fileName2, "r" );
-			if (_r_gzfp2 == NULL)
-			{
-				return 0;
-			}
-		}
-		else
-		{
-			_r_gzfp2 = _r_gzfp1;
-		}
-
-		readFirstSeq = &readFirstSeqGZ;
-		readSecondSeq = &readSecondSeqGZ;
-	}
-
-	if (ch == '>')
-		*fastq = 0;
-	else
-		*fastq = 1;
-
-	// Counting the number of lines in the file
-	while (readFirstSeq(dummy)) maxCnt++;
-
-	if (!compressed)
-	{
-		rewind(_r_fp1);
-	}
-	else
-	{
-		gzrewind(_r_gzfp1);
-	}
-
-	// Calculating the Maximum # of sequences
-	if (*fastq)
-	{
-		maxCnt /= 4;
-	}
-	else
-	{
-		maxCnt /= 2;
-	}
-
-	if (pairedEnd && fileName2 != NULL )
-		maxCnt *= 2;
-
-	list = getMem(sizeof(Read)*maxCnt);
-
-	while( readFirstSeq(name1) )
-	{
-		err1 = 0;
-		err2 = 0;
-		readFirstSeq(seq1);
-		name1[strlen(name1)-1] = '\0';
-
-		if ( *fastq )
-		{
-			readFirstSeq(dummy);
-			readFirstSeq(qual1);
-			qual1[strlen(qual1)-1] = '\0';
-		}
-		else
-		{
-			sprintf(qual1, "*");
-		}
-		
-		// Cropping
-		if (cropSize > 0)
-		{
-			seq1[cropSize] = '\0';
-			if ( *fastq )
-				qual1[cropSize] = '\0';
-		}
-
-
-		nCnt = 0;
-		for (i=0; i<strlen(seq1); i++)
-		{
-			seq1[i] = toupper (seq1[i]);
-			if (seq1[i] == 'N')
-			{
-				nCnt++;
-			}
-			else if (isspace(seq1[i]))
-			{
-
-				seq1[i] = '\0';
-				break;
-			}
-		}
-
-		if (nCnt > errThreshold)
-		{
-			err1 = 1;
-		}
-
-		// Reading the second seq of pair-ends
-		if (pairedEnd)
-		{
-			readSecondSeq(name2);
-			readSecondSeq(seq2);
-			name2[strlen(name2)-1] = '\0';
-			
-
-			if ( *fastq )
-			{
-				readSecondSeq(dummy);
-				readSecondSeq(qual2);
-
-				qual2[strlen(qual2)-1] = '\0';
-			}
-			else
-			{
-				sprintf(qual2, "*");
-			}
-			
-			
-			// Cropping
-			if (cropSize > 0)
-			{
-				seq2[cropSize] = '\0';
-				if ( *fastq )
-					qual2[cropSize] = '\0';
-			}
-
-
-			nCnt = 0;
-			for (i=0; i<strlen(seq2); i++)
-			{
-				seq2[i] = toupper (seq2[i]);
-				if (seq2[i] == 'N')
-				{
-					nCnt++;
-
-				}
-				else if (isspace(seq2[i]))
-				{
-					seq2[i] = '\0';
-				}
-			}
-			if (nCnt > errThreshold)
-			{
-				err2 = 1;
-			}
-
-
-			if (strlen(seq1) < strlen(seq2)) { 
-			  seq2[strlen(seq1)] = '\0'; 
-			  if ( *fastq )
-			    qual2[strlen(seq1)] = '\0'; 
-			  if (!clipped) clipped = 2; 
-			}
-			else if (strlen(seq1) > strlen(seq2)){
-			  seq1[strlen(seq2)] = '\0';
-			  if ( *fastq )
-			    qual1[strlen(seq2)] = '\0';
-			  if (!clipped) clipped = 1;
-			}
-
-			if (clipped == 1 || clipped == 2){
-			  fprintf(stdout, "[PE mode warning] Sequence lengths are different,  read #%d is clipped to match.\n", clipped);
-			  clipped = 3;
-			}
-			
-
-
-		}
-
-		if (!pairedEnd && !err1)
-		{
-			int _mtmp = strlen(seq1);
-                        list[seqCnt].hits = getMem (1+3*_mtmp+3+strlen(name1)+1);
-                        list[seqCnt].seq  = list[seqCnt].hits + 1;
-                        list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
-                        list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
-                        list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
-                        
-			list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
-                        list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
-
-			list[seqCnt].readNumber = seqCnt;			
-
-                        reverseComplete(seq1, rseq1, _mtmp);
-                        rseq1[_mtmp] =  '\0';
-                        int i;
-
-                        list[seqCnt].hits[0] = 0;
-
-                        for (i=0; i<=_mtmp; i++)
-                        {
-                                list[seqCnt].seq[i] = seq1[i];
-                                list[seqCnt].rseq[i] = rseq1[i] ;
-                                list[seqCnt].qual[i] = qual1[i];
-                        }
-		
-			
-                        //MAKE HASH VALUE
-                        short code = 0;
-
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
-                        list[seqCnt].hashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
-                        }
-
-
-                        code = 0;
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
-                        list[seqCnt].rhashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
-                        }
-			
-			int j = 0;
-			int tmpSize = _mtmp / (errThreshold+1);
-
-	                list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
-			for(i=0; i < errThreshold+1; i++)
-			{
-				code = 0;
-				for(j = 0; j < tmpSize; j++)
-				{
-					code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
-				}
-				list[seqCnt].hashValSampleSize[i] = code;	
-			}
-
-			sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
-
-			seqCnt++;
-
-		}
-		else if (pairedEnd && !err1 && !err2)
-		{
-
-			// Naming Conventions X/1, X/2 OR X
-			int tmplen = strlen(name1);
-			if (strcmp(name1, name2) != 0)
-			{
-				tmplen = strlen(name1)-2;
-			}
-		
-			//first seq
-			int _mtmp = strlen(seq1);
-			list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
-			list[seqCnt].seq = list[seqCnt].hits + 1;
-			list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
-			list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
-			list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
-
-			list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
-                        list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
-                  	list[seqCnt].readNumber = seqCnt;
-
-			reverseComplete(seq1, rseq1, _mtmp);
-			rseq1[_mtmp] =  '\0';
-			int i;
-
-			list[seqCnt].hits[0] = 0;
-
-			for (i=0; i<=_mtmp; i++)
-			{
-				list[seqCnt].seq[i] = seq1[i];
-				list[seqCnt].rseq[i] = rseq1[i] ;
-				list[seqCnt].qual[i] = qual1[i];
-			}
-
-
-			name1[tmplen]='\0';
-
-			//MAKE HASH VALUE
-                        short code = 0;
-
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
-                        list[seqCnt].hashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
-                        }
-
-
-                        code = 0;
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
-                        list[seqCnt].rhashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
-                        }
-
-                        int j = 0;
-                        int tmpSize = _mtmp / (errThreshold+1);
-
-                        list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
-                        for(i=0; i < errThreshold+1; i++)
-                        {
-                                code = 0;
-                                for(j = 0; j < tmpSize; j++)
-                                {
-                                        code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
-                                }
-                                list[seqCnt].hashValSampleSize[i] = code;
-                        }
-
-			sprintf(list[seqCnt].name,"%s%c", ((char*)name1)+1,'\0');
-
-
-			seqCnt++;
-
-			//second seq
-			list[seqCnt].hits = getMem (1+3*_mtmp+3+tmplen+1);
-			list[seqCnt].seq = list[seqCnt].hits + 1;
-			list[seqCnt].rseq = list[seqCnt].seq + _mtmp+1;
-			list[seqCnt].qual = list[seqCnt].rseq + _mtmp+1;
-			list[seqCnt].name = list[seqCnt].qual + _mtmp+1;
-
-			list[seqCnt].hashValue = getMem(sizeof(short)*_mtmp);
-                        list[seqCnt].rhashValue = getMem(sizeof(short)*_mtmp);
- 		 	list[seqCnt].readNumber = seqCnt;
-
-			reverseComplete(seq2, rseq2, _mtmp);
-			rseq2[_mtmp] =  '\0';
-
-			list[seqCnt].hits[0] = 0;
-
-			for (i=0; i<=_mtmp; i++)
-			{
-				list[seqCnt].seq[i] = seq2[i];
-				list[seqCnt].rseq[i] = rseq2[i] ;
-				list[seqCnt].qual[i] = qual2[i];
-			}
-
-
-			name2[tmplen]='\0';
-
-    		        //MAKE HASH VALUE
-                        code = 0;
-
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].seq[i]);
-                        list[seqCnt].hashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].hashValue[i] = (list[seqCnt].hashValue[i-1] - 125 * CHARCODE(seq1[i-1])) * 5 + CHARCODE(seq1[i+3]);
-                        }
-
-
-                        code = 0;
-                        for(i=0; i < 4; i++)
-                                code = code * 5 + CHARCODE(list[seqCnt].rseq[i]);
-                        list[seqCnt].rhashValue[0] = code;
-
-
-                        for(i = 1; i < _mtmp-3; i++)
-                        {
-                                list[seqCnt].rhashValue[i] = (list[seqCnt].rhashValue[i-1] - 125 * CHARCODE(rseq1[i-1])) * 5 + CHARCODE(rseq1[i+3]);
-                        }
-
-                        j = 0;
-                        tmpSize = _mtmp / (errThreshold+1);
-
-                        list[seqCnt].hashValSampleSize = getMem(sizeof(int)*(errThreshold+1));
-                        for(i=0; i < errThreshold+1; i++)
-                        {
-                                code = 0;
-                                for(j = 0; j < tmpSize; j++)
-                                {
-                                        code = code * 5 + CHARCODE(list[seqCnt].seq[i*tmpSize+j]);
-                                }
-                                list[seqCnt].hashValSampleSize[i] = code;
-                        }
-	
-			sprintf(list[seqCnt].name,"%s%c", ((char*)name2)+1,'\0');
-
-			seqCnt++;
-
-		}
-		else
-		{
-			discarded++;
-		}
-	}
-
-	if (seqCnt > 0)
-	{
-		SEQ_LENGTH = strlen(list[0].seq);
-	}
-	else
-	{
-		fprintf(stdout, "ERROR: No reads can be found for mapping\n");
-		return 0;
-	}
-
-
-	// Closing Files
-	if (!compressed)
-	{
-		fclose(_r_fp1);
-		if ( pairedEnd && fileName2 != NULL )
-		{
-			fclose(_r_fp2);
-		}
-	}
-	else
-	{
-		gzclose(_r_gzfp1);
-		if ( pairedEnd && fileName2 != NULL)
-		{
-			gzclose(_r_fp2);
-		}
-	}
-
-	//qsort(list, seqCnt, sizeof(Read), toCompareRead);
-
-	adjustQual(list, seqCnt);
-
-	*seqList = list;
-	*seqListSize = seqCnt;
-	
-
-	_r_seq = list;
-	_r_seqCnt = seqCnt;
-
-	if ( pairedEnd ) discarded *= 2;
-
-	if (seqCnt>1)
-	  fprintf(stdout, "%d sequences are read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
-	else
-	  fprintf(stdout, "%d sequence is read in %0.2f. (%d discarded) [Mem:%0.2f M]\n", seqCnt, (getTime()-startTime), discarded, getMemUsage());
-
-
-
-	return 1;
-}
-/**********************************************/
-void loadSamplingLocations(int **samplingLocs, int * samplingLocsSize)
-{
-	int i;
-	int samLocsSize = errThreshold + 1;
-	int *samLocs = getMem(sizeof(int)*samLocsSize);
-
-	for (i=0; i<samLocsSize; i++)
-	{
-		samLocs[i] = (SEQ_LENGTH / samLocsSize) *i;
-		if ( samLocs[i] + WINDOW_SIZE > SEQ_LENGTH)
-			samLocs[i] = SEQ_LENGTH - WINDOW_SIZE;
-	}
-
-	// Outputing the sampling locations
-
-	/*
-
-	int j;
- 	for (i=0; i<SEQ_LENGTH; i++)
-	{
-		fprintf(stdout, "-");
-	}
-	fprintf(stdout, "\n");
-
-	for ( i=0; i<samLocsSize; i++ )
-	{
-		for ( j=0; j<samLocs[i]; j++ )
-		{
-			fprintf(stdout," ");
-		}
-		for (j=0; j<WINDOW_SIZE; j++)
-		{
-			fprintf(stdout,"+");
-		}
-		fprintf(stdout, "\n");
-		fflush(stdout);
-	}
-	
-
-	for ( i=0; i<SEQ_LENGTH; i++ )
-	{
-		fprintf(stdout, "-");
-	}
-	fprintf(stdout, "\n");
-
-	*/
-
-	*samplingLocs = samLocs;
-	*samplingLocsSize = samLocsSize;
-	_r_samplingLocs = samLocs;
-}
-
-void finalizeReads(char *fileName)
-{
-	FILE *fp1=NULL;
-
-	if (fileName != NULL)
-	{
-		fp1 = fileOpen(fileName, "w");
-	}
-	if (pairedEndMode)
-		_r_seqCnt /=2;
-
-	int i=0;
-	for (i = 0; i < _r_seqCnt; i++)
-	{
-		if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0  &&  strcmp(_r_seq[2*i].qual,"*")!=0)
-		{
-			fprintf(fp1,"@%s/1\n%s\n+\n%s\n@%s/2\n%s\n+\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].qual, _r_seq[i*2].name, _r_seq[i*2+1].seq, _r_seq[i*2+1].qual);
-		}
-		else if (pairedEndMode && _r_seq[2*i].hits[0] == 0 && _r_seq[2*i+1].hits[0] == 0)
-		{
-			fprintf(fp1, ">%s/1\n%s\n>%s/2\n%shits=%d\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq, _r_seq[2*i+1].hits[0]);
-		}
-		else if (!pairedEndMode && _r_seq[i].hits[0] == 0 && strcmp(_r_seq[i].qual, "*")!=0)
-		{
-			fprintf(fp1,"@%s\n%s\n+\n%s\n", _r_seq[i].name, _r_seq[i].seq, _r_seq[i].qual);
-		}
-		else if (!pairedEndMode && _r_seq[i].hits[0] == 0)
-		{
-			fprintf(fp1,">%s\n%s\n", _r_seq[i].name, _r_seq[i].seq);
-		}
-	}
-
-	fclose(fp1);
-	if (pairedEndMode)
-		_r_seqCnt *= 2;
-
-	for (i = 0; i < _r_seqCnt; i++)
-	{
-		freeMem(_r_seq[i].hits,0);
-	}
-
-
-	freeMem(_r_seq,0);
-	freeMem(_r_samplingLocs,0);
-}
-
-void adjustQual(Read *list, int seqCnt){
-  /* This function will automatically determine the phred_offset and readjust quality values if needed */
-}
-
-
-
-/*void finalizeOEAReads(char *fileName)
-{
-	FILE *fp1=NULL;
-	FILE *fp2=NULL;
-	
-	//printf("OEA%s\n", fileName);
-	char fileNameOEA1[200];
-	char fileNameOEA2[200];
-	sprintf(fileNameOEA1, "%s_OEA1", fileName);
-	sprintf(fileNameOEA2, "%s_OEA2", fileName);
-	
-	
-	if (fileName != NULL)
-	{
-		fp1 = fileOpen(fileNameOEA1, "w");
-		fp2 = fileOpen(fileNameOEA2, "w");
-	}
-	if (pairedEndMode)
-		_r_seqCnt /=2;
-
-	int i=0;
-	printf("%d\n", _r_seqCnt);
-	for (i = 0; i < _r_seqCnt; i++)
-	{
-		if (pairedEndMode && _r_seq[2*i].hits[0] == 0 &&  _r_seq[2*i+1].hits[0] != 0 && strcmp(_r_seq[2*i].qual, "*")==0)
-		{
-			fprintf(fp1,">%s/1\n%s\n>%s/2\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq);
-		}
-		else if (pairedEndMode && _r_seq[2*i].hits[0] != 0 && _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual, "*")==0)
-		{
-			fprintf(fp2, ">%s/1\n%s\n>%s/2\n%s\n", _r_seq[i*2].name, _r_seq[i*2].seq, _r_seq[i*2].name, _r_seq[i*2+1].seq);
-		}
-		else if (pairedEndMode && _r_seq[2*i].hits[0] == 0 &&  _r_seq[2*i+1].hits[0] != 0 && strcmp(_r_seq[2*i].qual, "*")!=0)
-		{
- 		fprintf(fp1,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name, 
-									_r_seq[2*i].seq, 
-									_r_seq[2*i].qual,  
-									_r_seq[2*i+1].name, 
-									_r_seq[2*i+1].seq, 
-									_r_seq[2*i+1].qual);
-		}
-		else if ( pairedEndMode && _r_seq[2*i].hits[0] != 0 &&  _r_seq[2*i+1].hits[0] == 0 && strcmp(_r_seq[2*i].qual, "*")!=0  )
-		{
-			 fprintf(fp2,"@%s\n%s\n+\n%s\n@%s\n%s\n+\n%s\n", _r_seq[2*i].name, 
-                                                                        _r_seq[2*i].seq, 
-                                                                        _r_seq[2*i].qual,  
-                                                                        _r_seq[2*i+1].name,
-                                                                        _r_seq[2*i+1].seq,
-                                                                        _r_seq[2*i+1].qual);
-		}
-	}
-
-	fclose(fp1);
-	fclose(fp2);
-
-}*/