--- a/mrfast-2.1.0.4/MrFAST.h	Tue Feb 21 10:29:47 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,209 +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
- */
-
-
-
-#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