--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrsfast-2.3.0.2/MrsFAST.h	Tue Feb 21 10:39:28 2012 -0500
@@ -0,0 +1,103 @@
+/*
+ * 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
+ */
+
+
+#ifndef __MRS_FAST__
+#define __MRS_FAST__
+
+#include "Reads.h"
+
+#define MAP_CHUNKS 15
+
+// Pair is used to pre-processing and making the read index table
+typedef struct
+{
+	int hv;
+	int seqInfo;
+} Pair;
+
+typedef struct
+{
+	int hv;
+	unsigned int *seqInfo;
+} ReadIndexTable;
+
+
+typedef struct mn
+{
+	int loc;
+	char dir;
+	char err;
+	float score;
+	char md[40];
+	char chr[10];
+} FullMappingInfo;
+
+typedef struct lc
+{
+	int loc[MAP_CHUNKS];
+	struct lc *next;
+} MappingLocations;
+
+typedef struct inf
+{
+	int size;
+	MappingLocations *next;
+} MappingInfo;
+
+typedef struct 
+{
+	FILE * fp;
+	char name[400];
+} FILE_STRUCT;
+
+extern long long			verificationCnt;
+extern long long			mappingCnt;
+extern long long			mappedSeqCnt;
+extern long long			completedSeqCnt;
+
+void initFAST(	Read *seqList,
+				int seqListSize,
+				int *samplingLocs,
+				int samplingLocsSize, 
+				char *fileName);
+
+void finalizeFAST();
+
+int mapSingleEndSeq();
+int mapPaiedEndSeq();
+void outputPairedEnd();
+void outputPairedEndDiscPP();
+#endif