--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mrfast-2.1.0.5/MrFAST.h	Fri Mar 09 07:35:51 2012 -0500
@@ -0,0 +1,209 @@
+/*
+ * 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 __MR_FAST__
+#define __MR_FAST__
+
+#include "Reads.h"
+
+#define MAP_CHUNKS 15
+#define MAX_CIGAR_SIZE 100
+
+
+// Pair is used to pre-processing and making the read index table
+typedef struct
+{
+	int hv;
+	//char hv[50];
+	int readNumber;
+} Pair;
+
+typedef struct
+{
+	int hv;
+	unsigned int *seqInfo;
+} ReadIndexTable;
+
+
+typedef struct 
+{
+	int loc;
+	char dir;
+	int err;
+	float score;
+	char md[MAX_CIGAR_SIZE];
+	char chr[20];
+	char cigar[MAX_CIGAR_SIZE];
+	int cigarSize;
+	int mdSize;
+} FullMappingInfo;
+
+typedef struct
+{
+	int loc;
+	char dir;
+	int err;
+	float score;
+	char md[MAX_CIGAR_SIZE];
+	char chr[20];
+	char cigar[MAX_CIGAR_SIZE];
+	int cigarSize;
+	int mdSize;
+} BestFullMappingInfo;
+
+typedef struct lc
+{
+	char md[MAP_CHUNKS][MAX_CIGAR_SIZE];
+	int mdSize[MAP_CHUNKS];
+
+	char cigar[MAP_CHUNKS][MAX_CIGAR_SIZE];
+	int cigarSize[MAP_CHUNKS];
+
+	int err[MAP_CHUNKS];
+	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;
+
+typedef struct 
+{
+	FullMappingInfo *mi;
+	int size;
+} FullMappingInfoLink;
+
+
+typedef struct
+{
+	char readString[200];	
+	char ref[200];
+	int err;
+	char matrix[200];
+} extraCaching;
+
+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 initVerifiedLocs();
+void initLookUpTable();
+void initBestMapping();
+void initBestConcordantDiscordant(int readNumber);
+
+void finalizeFAST();
+void finalizeBestSingleMapping();
+void finalizeBestConcordantDiscordant();
+void finalizeOEAReads(char *);
+
+
+int mapAllSingleEndSeq();
+void mapSingleEndSeq(unsigned int *l1, int s1, int readNumber, int readSegment, int direction);
+void mapPairedEndSeqList(unsigned int *l1, int s1, int readNumber, int readSegment, int direction);
+
+void mapPairedEndSeq();
+
+void outputPairedEnd();
+void outputPairedEndDiscPP();
+
+
+void outputPairFullMappingInfo(FILE *fp, int readNumber);
+void setPairFullMappingInfo(int readNumber, FullMappingInfo mi1, FullMappingInfo mi2);
+void setFullMappingInfo(int readNumber, int loc, int dir, int err, int score, char *md, char * refName, char *cigar);
+
+void outputAllTransChromosal();
+void outputTransChromosal(char *fileName1, char *fileName2, FILE * fp_out);
+
+void generateSNPSAM(char *matrix, int matrixLength, char *outputSNP);
+void generateCigar(char *matrix, int matrixLength, char *cigar);
+void generateCigarFromMD(char *mistmatch, int mismatchLength, char *cigar);
+
+int msfHashVal(char *seq);
+
+int backwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
+int forwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
+
+int forwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb);
+int backwardEditDistanceSSE2G(char *a, int lena, char *b,int lenb);
+
+int forwardEditDistance4SSE2(char *a, int lena, char *b,int lenb);
+int backwardEditDistance4SSE2(char *a, int lena, char *b,int lenb);
+
+int forwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb);
+int backwardEditDistanceSSE2Extention(char *a, int lena, char *b,int lenb);
+
+
+/***********************************/
+
+int editDistance(int refIndex, char *seq, int seqLength, char *matrix);
+
+int verifySingleEndEditDistance(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, 
+				char *matrix, int *map_location, short *seqHashValue);
+
+int verifySingleEndEditDistance2(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, 
+				char *matrix, int *map_location, short *seqHashValue);
+
+int verifySingleEndEditDistance4(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength, 
+				char *matrix, int *map_location, short *seqHashValue);
+
+int verifySingleEndEditDistanceExtention(int refIndex, char *lSeq, int lSeqLength, char *rSeq, int rSeqLength, int segLength,
+                                char *matrix, int *map_location, short *seqHashValue);
+
+#endif