--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrfast-2.1.0.5/Common.c	Fri Mar 09 07:35:51 2012 -0500
@@ -0,0 +1,184 @@
+/*
+ * 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');
+	}
+}