--- 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