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SirFAST.h
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SirFAST.h
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/*
* Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent 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 cs DOT bilkent DOT edu DOT tr
*/
#ifndef __MR_FAST__
#define __MR_FAST__
#include "Reads.h"
#include <ctype.h>
#define MAP_CHUNKS 15
#define MAX_CIGAR_SIZE 100
#define MAX_CG_SIZE 20
// 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 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[MAX_CIGAR_SIZE];
char cigar[MAX_CIGAR_SIZE];
int cigarSize;
int mdSize;
double tprob;
} BestFullMappingInfo;
typedef struct lc
{
char md[MAP_CHUNKS][MAX_CG_SIZE];
int mdSize[MAP_CHUNKS];
char cigar[MAP_CHUNKS][MAX_CG_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
{
FullMappingInfo *mi;
int size;
} FullMappingInfoLink;
extern long long verificationCnt;
extern long long mappingCnt;
extern long long mappedSeqCnt;
extern long long completedSeqCnt;
void initFAST(Read *, int, int *, int, char *);
void initVerifiedLocs();
void initLookUpTable();
void finalizeFAST();
void finalizeBestSingleMapping();
void finalizeBestConcordantDiscordant();
//void finalizeOEAReads(char *);
int mapAllSingleEndSeq();
void generateCigarFromMD(char *, int, char *);
int msfHashVal(char *);
int backwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
int forwardEditDistance2SSE2(char *a, int lena, char *b,int lenb);
double mapProb(int, char *, int, int);
int mapQ(int);
/***********************************/
// for fastHASH
int compareEntrySize (const void *a, const void *b); // fastHASH()
void mapSingleEndSeq(unsigned int *l1, int s1, int readNumber, int readSegment, int direction, // fastHASH()
int index, key_struct* keys_input, int potential_key_number); // fastHASH()
void mapPairEndSeqList(unsigned int *l1, int s1, int readNumber, int readSegment, int direction,// fastHASH()
int index, key_struct* keys_input, int potential_key_number); // fastHASH(
void mapPairedEndSeq();
//void outputPairedEnd();
int outputPairedEnd(int pre_unmappedCnt);
void setFullMappingInfo(int readNumber, int loc, int dir, int err, int score,
char *md, char * refName, char *cigar);
void outputAllTransChromosomal(int flag);
//void outputPairedEndDiscPP();
// sirFAST
void initFASTCG(Read *seqList, int seqListSize, int accSeqListSize);
void preProcessReadsCG();
void mapAllSingleEndSeqCG();
int searchKeyCG(int target_coor, unsigned int* entry_coor, int entry_size, int range);
void mapSingleEndSeqCG_forward(unsigned int *l1, int s1, int readNumber, int readSegment, int index, key_struct* key_input, int direction, int num_base, int num_key, int num_ver, int num_ext);
void mapSingleEndSeqCG_reverse(unsigned int *l1, int s1, int readNumber, int readSegment, int index, key_struct* key_input, int direction, int num_base, int num_key, int num_ver, int num_ext);
void mapPairEndSeqCG_forward(unsigned int *l1, int s1, int readNumber, int readSegment, int index, key_struct* key_input, int direction, int num_base, int num_key, int num_ver, int num_ext);
void mapPairEndSeqCG_reverse(unsigned int *l1, int s1, int readNumber, int readSegment, int index, key_struct* key_input, int direction, int num_base, int num_key, int num_ver, int num_ext);
void printoutCG_forward(int genLoc, int * af_offset, char * seq, int error);
void printoutCG_reverse(int genLoc, int * af_offset, char * seq, int error);
int verifySingleEndCG(int refIndex, int readIndex, char* seq, int * af_offset, int variable, int length);
int verifySingleEndSeqCG_backward(int * locs, int * af_offset, char * seq1, key_struct* key_input, int index, int num_base, int num_key, int num_ver, int num_ext);
int verifySingleEndSeqCG_forward(int * locs, int * af_offset, char * seq1, key_struct* key_input, int index, int num_base, int num_key, int num_ver, int num_ext);
void generateAlignmentMatrxCG_backward(int genLoc, int * af_offset, char * seq, int error, char * matrix);
void generateAlignmentMatrxCG_forward(int genLoc, int * af_offset, char * seq, int error, char * matrix);
void resetFAST(unsigned int seqListSize);
FILE * initOEAReads();
void finalizeOEAReads(FILE * _fp_oea);
void performOEAReads(FILE * _fp_oea);
FILE * initPairedEndDiscPP();
void finalizePairedEndDiscPP(FILE * _fp_divet);
void performPairedEndDiscPP(FILE * _fp_divet);
void initBestMapping();
void performBestMapping(int readCnt);
void finalizeBestMapping(int readCnt);
void mapPairedEndSeqCG();
void initKeyInput(key_struct* key_input, int* key_hash);
void initForwardParam();
void initReverseParam();
/**************************************************************************************************/
#endif