/
analysisFunction.h
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/
analysisFunction.h
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#include <zlib.h>
#ifndef _angsd_
#define _angsd_
#define FOR(i,n) for(i=0; i<n; i++)
#include <cmath>
#include <vector>
#include "shared.h"
#include "chisquare.h"
#include <htslib/bgzf.h>
extern int refToInt[256];
extern char intToRef[5];
extern char intToIupac[15];
extern char refToChar[256];
namespace angsd {
double lbico(double n, double k);
double myComb2(int k,int r, int j);
//assuming samtools ordering
static int majorminor[4][4] =
{
{0,1,2,3},
{1,4,5,6},
{2,5,7,8},
{3,6,8,9}
};
template<typename T>
struct Matrix {
int x;
int y;
T **matrix;
};
template<typename T>
struct doubleTrouble {
int x0;
int y0;
T **matrix0;
int isBinary;
int x1;
int y1;
T **matrix1;
};
void norm(double *d,size_t len);
double getMax(double a,double b, double c);
double addProtect2(double a,double b);
double addProtect3(double a,double b, double c);
double addProtectN(double a[],int N);
Matrix<double> getMatrix(const char *name,int doBinary,int lens);
Matrix<int> getMatrixInt(const char *name,int lens);
int fexists(const char* str);
double sigm(double x);
double **get3likes(funkyPars *pars);
double **get3likesRescale(funkyPars *pars);
double **get3likes(funkyPars *pars,int *keepInd);
double **get3likesRMlow(funkyPars *pars,int *keepInd);
double **getlikes(funkyPars *pars,int *keepInd);
void swapDouble (double& first, double& second);
int matinv( double x[], int n, int m, double space[]);
void deleteMatrix(Matrix<double> mat);
void deleteMatrixInt(Matrix<int> mat);
void printMatrix(Matrix<double> mat,FILE *file);
doubleTrouble<double> getSample(const char *name,int lens, char* whichPhe, char* whichCov);
void deleteDoubleTrouble(doubleTrouble<double> dT);
void printDoubleTrouble(doubleTrouble<double> dT,FILE *file);
void logrescale(double *ary,int len);
int svd_inverse(double mat[],int xLen, int yLen);
double dnorm(double x,double mean,double sd,int ifLog);
double bernoulli(int k, double p, int ifLog);
double sd(double* phe, int size );
double poisson(double k, double lambda, int ifLog);
double to_pval(Chisqdist *chisq,double f);
char *strpop(char **str,char split);
int getRandomCount(suint *d, int i, int depth = -1);
int getMaxCount(suint *d, int i, int depth = -1);
int getIupacCount(suint *d, int i, double iRatio, int depth = -1);
int getRandomCountTotal(suint *d, int nInd);
int getMaxCountTotal(suint *d, int nInd);
int getIupacCountTotal(suint *d, int nInd, double iRatio);
double estFreq(double *loglike,int numInds);
template <typename T>
T * allocArray(size_t len,T defval){
T *ret= new T[len];
for(size_t i=0;i<len;i++)
ret[i]=defval;
return ret;
}
template <typename T>
T * allocArray(size_t len){
T *ret= new T[len];
return ret;
}
template <typename T>
T sum(const T *ary,size_t len){
T s =0;
for(size_t i=0;i<len ; i++)
s+=ary[i];
// printf("sum:%f\n",s);
return s;
}
void print_array(FILE *fp,double *ary,int len);
void print_array(FILE *fp,int *ary,int len);
double *readDouble(const char*fname,int hint);
int whichMax(double *d,int len);
}
#endif
double phi(double x);