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/*
* SweeD
*
* Copyright September 2012 by Nikolaos Alachiotis and Pavlos Pavlidis
*
* This program is free software; you may redistribute it and/or modify its
* under the terms of the GNU General Public License as published by the Free
* Software Foundation; either version 2 of the License, or (at your option)
* any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
* for more details.
*
* For any other enquiries send an email to
* Pavlos Pavlidis (pavlidisp@gmail.com) or
* Nikolaos Alachiotis (n.alachiotis@gmail.com)
*
*/
#ifndef _SweeD_H
#define _SweeD_H
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <math.h>
#include <time.h>
#include <sys/time.h>
#include <limits.h>
#include "SweeD_BFGS.h"
#ifdef _USE_PTHREADS
#include <pthread.h>
#include <unistd.h>
#define EXIT 127
#define BUSYWAIT 0
#define LIKSFS 1
#define COMPRVLUT 2
#define COMPALPHA 3
#endif
#ifdef _DO_CHECKPOINTS
#include "dmtcpaware.h"
#endif
#ifdef _ANALYTICAL_SFS
#include <mpfr.h>
#include <float.h>
#define ACC 10000
#define APPROX 0
#define TOLTIME 1e-7
#define RESCALE 1
#endif
#define ENTRIES_PER_INT 32
#define DENOMINATOR_OFFSET 0.00001
#define REGISTER_WIDTH 32
#define MAXSIZE 10000
#define INFILENAMESIZE 1000
#define SEQNAMESIZE 1000
#define DECREASE 0.99
#define MINSNPPERWINDOW 5
#define STRINGLENGTH 100
#define VCF_HLENGTH 9 // number of fields in the VCF header line
#define MAX_CHROM_NAME_VCF 100
#define MAX_STATES_VCF 5
#define RESULTS_DEFAULT 0
#define RESULTS_ALL 1
#define RSQUARE 0
#define DOM 1
#define ABSDOM 2
#define JUSTD 3
#define ABSD 4
#define ABSDOM2 5
#define ZERO '0'
#define ONE '1'
#define GAP '-'
#define AD 'A'
#define CY 'C'
#define GU 'G'
#define TH 'T'
#define UN 'N'
#define BINARY 2
#define BINARY_WITH_GAPS 3
#define DNA 4
#define DNA_WITH_GAPS 5
#define STATESALL 8
#define OTHER_FORMAT -1
#define MS_FORMAT 0
#define FASTA_FORMAT 1
#define MACS_FORMAT 2
#define VCF_FORMAT 3
#define SF_FORMAT 4
#define INTOKS 8
#define N_REF 2
#define N_ALT 3
#define N_INFO 6
#define MAX_STATES 100
#define MAXINT 2147483647
char bits_in_16bits [0x1u << 16];
int linkage_disequilibrium;
int borderTol;
int VCF_header_lines;
char VCF_alignment_name [MAX_CHROM_NAME_VCF];
int VCF_first_SNP;
int nxtVCFalignment;
char runName[INFILENAMESIZE];
typedef float cor_t;
cor_t ABS (cor_t input);
double mainTime0;
int map[INTOKS];
int nofTokens;
int nofSamples;
typedef int al_t;
typedef double t_sfs;
struct pattern
{
int x;
int n;
unsigned char f;
int c;
struct pattern * nxt;
};
typedef struct
{
al_t *n; // number of valid bases in every site
al_t *n_t; // number of valid bases in every site
al_t *x; // number of derived bases in every site
al_t *x_t; // number of derived bases in every site
float * positions;
int * positionsInd;
int * p_t;
unsigned char *folded;
unsigned char *f_t;
unsigned char userSetFolded;
unsigned char userSFS;
char* outgroupSequence;
char* outgroupName;
int outgroupIndex;
int sequences;
int foldedFormat; // if outgroup exists we set this to zero
int segsites;
int length;
int minn;
int minx;
int maxn;
int maxx;
al_t * stateA;
al_t * stateC;
al_t * stateG;
al_t * stateT;
t_sfs * SFS;
t_sfs * tmpSFS;
int startSFS;
int endSFS;
int * ng;
t_sfs * lb;
t_sfs * ub;
int params;
al_t * n_pat;
al_t * x_pat;
unsigned char * f_pat;
int * c_pat;
int patterns;
t_sfs *** gridProbs;
t_sfs * gridADs;
t_sfs interval;
t_sfs logAD0;
t_sfs * baseLikelihood;
struct pattern * patternList;
float sweepStep;
int discSites;
#ifdef _USE_PTHREADS
t_sfs * threadScoresLIKSFS;
#endif
} alignment_struct;
alignment_struct * alignment;
double * rv;
double ** rvLUT;
double ** rvLUT2;
#define GRIDSIZE 300
#define LOCALGRIDSIZE 100
double div6;
typedef struct
{
double * val;
int * sc;
} factorial_LUT;
factorial_LUT * factLUT;
typedef struct
{
int sfRealPos;
t_sfs likelihood;
t_sfs alpha;
} clr_struct;
clr_struct * clr;
#ifdef _ANALYTICAL_SFS
typedef struct
{
double t;
double d;
} event;
int eventsTotal;
event * eventList;
mpfr_t ** analyticalSFS_LUT;
void computeAnalyticalSFS(int sequences, FILE * fp);
void computeAnalyticalSFSExpo(int sequences, double R, FILE * fpSFSo);
long double xExponential_Integral_Ei( long double x );
void mpfr_Exponential_Integral_Ei( mpfr_t EImp, mpfr_t xmp );
#endif
void printHeading (FILE * fp);
void computeCorrelationMatrixPairwise(alignment_struct * alignment, clr_struct * omega, int omegaIndex, int firstRowIndex, void * threadData, cor_t ** myCorrelationMatrix, char * lookuptable);
void applyCorrelationMatrixAdditions (clr_struct * omega, int omegaIndex, int firstRowIndex, cor_t ** correlationMatrix);
void overlapCorrelationMatrixAdditions (alignment_struct * alignment, clr_struct * omega, int lvw_i, int cvw_i, int * firstRowToCopy, int * firstRowToCompute, int * firstRowToAdd);
void shiftCorrelationMatrixValues (clr_struct * omega, int lvw_i, int cvw_i, int firstRowToCopy, cor_t ** correlationMatrix);
void commandLineParser(int argc, char** argv,
char * infile,
char * sfsfile,
char * sfsofile,
char * sfofile,
int * grid,
int * length,
unsigned int * seed,
int * fileFormat,
int * results,
char * outgroupName,
unsigned char *userSetFolded,
unsigned char * userSFS,
unsigned char * onlySFS,
unsigned char * onlySF,
int * monomorphic,
int * threads,
int * sequences,
int * analyticalSFS,
double *growthRate);
void removeMonomorphicSites (int monomorphic, FILE * fp);
t_sfs computeBaseLikelihood();
t_sfs getAlpha (int sweepPosition, t_sfs * likelihood);
int isBinary(char input);
void printIntArray(int *array, int n);
void printUCharArray(unsigned char *array, int n);
void printFloatArray(float *array, int n);
void printCharArray(char *array, int n);
int isEndOfLine(char ent);
void goToLineEnd(FILE *fp);
int findFirstAlignment(FILE *fp, int format);
int findNextAlignment(FILE *fp, int fileFormat);
void freeAlignment();
void readAlignment(FILE *fp, int format, FILE * fpInfo, FILE * sfO);
void compressAlignment(alignment_struct *alignment);
void knuthShuffle(int orgArray[], int arraySize, int start, int end);
int parseSample(FILE *fp, int targetTok, char **word, int *wordLength, int curTok);
void unGetChars(FILE *fp, char* chars, int n);
int isValidDNACharacter(char input);
void parseIndividual(char *word, char** genotype, char delimiter, int token, char* states, char phased, char unphased, int *ploidy, int *max_ploidy);
void ignoreAll(FILE * fp, char * ent);
int isSpace(char ent);
double XchooseY_ln(int x, int y);
void checkSNIPPositions (FILE* fp, alignment_struct * alignment, int index);
void createSFS (FILE * fpSFS, FILE * fpSFSo, int alignmentIndex, int * SFSsize);
void createCLR (int grid);
void createPROBS (int probGrid);
void createPatterns(void);
void computeFactLUT(void);
double gettime(void);
t_sfs likelihoodSFS_SNP(t_sfs * tmpSFS, int x, int n, unsigned char f, int c);
void updateSF(FILE * fpSFo);
#ifdef _USE_PTHREADS
typedef struct
{
int threadID;
int threadTOTAL;
int threadBARRIER;
int threadOPERATION;
}threadData_t;
pthread_t * workerThreadL;
threadData_t * threadDataL;
int gridP;
void likelihoodSFS_thread(int tid, int threads);
void parallelComputationRVLUT_thread(int tid, int threads);
void computeAlpha_parallel(int grid);
void parallelComputationAlpha_thread(int tid, int threads);
void syncThreadsBARRIER();
#endif
#ifdef _DO_CHECKPOINTS
double lastCheckpointTime;
double checkPointInterval;
extern void writeCheckpoint();
#endif
#endif
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