--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrsfast-2.3.0.2/RefGenome.c	Tue Feb 21 10:39:28 2012 -0500
@@ -0,0 +1,161 @@
+/*
+ * Copyright (c) <2008 - 2009>, 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 name of the <ORGANIZATION> 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.
+ */
+
+/*
+ * Author         : Faraz Hach
+ * Email          : fhach AT cs DOT sfu
+ * Last Update    : 2009-12-08
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "Common.h"
+#include "RefGenome.h"
+
+FILE *_rg_fp;
+char *_rg_gen;
+char *_rg_name;
+int _rg_offset;
+int _rg_contGen; 
+
+/**********************************************/
+int initLoadingRefGenome(char *fileName)
+{
+	char ch;
+	_rg_fp = fileOpen (fileName, "r");
+	if (fscanf(_rg_fp, "%c", &ch))
+	{
+		if (ch == '>')
+		{
+			_rg_contGen = 0;
+			_rg_offset = 0;
+			_rg_gen = getMem(CONTIG_MAX_SIZE);
+			_rg_name = getMem(CONTIG_NAME_SIZE);
+			return 1;
+		}
+	}
+	return 0;
+}
+/**********************************************/
+void finalizeLoadingRefGenome()
+{
+	freeMem(_rg_gen, CONTIG_MAX_SIZE);
+	freeMem(_rg_name, CONTIG_NAME_SIZE); 
+	fclose(_rg_fp);
+}
+/**********************************************/
+int loadRefGenome(char **refGen, char **refGenName, int *refGenOff)
+{
+	char ch;
+	int i;
+	int returnVal = 0;
+	int actualSize=0;
+	int size;
+	char *tmp;
+	
+	// New Conting 
+	if (!_rg_contGen)
+	{
+		size = 0;
+		tmp = fgets(_rg_name, SEQ_MAX_LENGTH, _rg_fp);
+		int k;
+		for (k=0; k<strlen(_rg_name);k++)
+		{
+			if (_rg_name[k] == ' ')
+			{
+				_rg_name[k]='\0';
+				break;
+			}
+		}
+			
+	}
+	else
+	{
+		size=strlen(_rg_gen);
+		for( i = 0 ; i < CONTIG_OVERLAP ; i++ )
+		{
+			
+			_rg_gen[i] = _rg_gen[size-CONTIG_OVERLAP+i];
+			if (_rg_gen[i] != 'N')
+				actualSize++;
+		}
+		size = CONTIG_OVERLAP;
+	}
+	while( fscanf(_rg_fp, "%c", &ch) > 0 )
+	{
+		if (ch == '>')
+		{
+			_rg_contGen = 0;
+			returnVal = 1;
+			break;
+		}
+		else if (!isspace(ch))
+		{
+			ch = toupper(ch);
+			_rg_gen[size++] = ch;
+			if (ch != 'N')
+			{
+				actualSize++;
+			}
+			if (actualSize == CONTIG_SIZE || size == CONTIG_MAX_SIZE)
+			{
+				_rg_contGen = 1;
+				returnVal=1;
+				break;
+			}
+		}
+
+	}
+
+	_rg_gen[size] = '\0';
+	for (i=strlen(_rg_name)-1; i >= 0; i--)
+		if (!isspace(_rg_name[i]))
+			break;
+	_rg_name[i+1] = '\0';
+
+	*refGenOff = _rg_offset;
+	*refGenName = _rg_name;
+	*refGen = _rg_gen;
+
+	if (_rg_contGen == 1)
+	{
+		_rg_offset += size-CONTIG_OVERLAP;
+	}
+	else
+	{
+		_rg_offset = 0;
+	}
+	
+	
+	return returnVal;
+}
+/**********************************************/