--- 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');
-	}
-}