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#include <ctype.h>
#include <nicklib.h>
#include <xsearch.h>
#define IDSIZE 40
#ifndef ADMUTILS
typedef struct
{
char ID[IDSIZE];
char *egroup;
char gender; /* 'M' or 'F' */
double theta_mode; /* most likely theta on mesh */
double lambda_mode; /* mean of log10(lambda) from probability distribution */
double Xtheta_mode; /* most likely theta on mesh */
double Xlambda_mode; /* most likely lambda on mesh */
int idnum;
int affstatus; /* affected status */
int ignore; /* YES => do not use */
int flag;
double thetatrue;
double Xthetatrue;
double lambdatrue;
double Xlambdatrue;
double totgamms[3];
double totscore;
double rawqval;
double qval;
} Indiv;
typedef struct
{
char ID[IDSIZE];
int chrom;
char cchrom[6];
double genpos;
double physpos;
double aa_cauc_freq; /* frequencies in ancestral pop to AA */
double aa_af_freq;
double cauc_freq; /* frequencies of variant allele */
double af_freq;
double cftrue;
double aftrue;
double aa_cftrue;
double aa_aftrue;
int markernum; /* marker number */
char *pbuff;
char *ebuff; /* for random ethnic path */
int isfake; /* 1 if fake marker else 0 */
int isrfake;
/* real marker treated as fake. Used for 2D scoring */
int ignore;
int ngtypes; /* number of gtypes */
int *gtypes;
int af_nn[2];
int cauc_nn[2];
double *modelscores;
double *totmodelscores;
double score;
double weight;
double estgenpos;
double estdis;
double dis;
double esum;
double lsum;
double gpsum;
double gpnum;
void *pcupt;
int tagnumber;
char alleles[2];
int chimpfudge;
} SNP;
typedef struct
{
char ID[IDSIZE];
Indiv *father;
Indiv *mother;
Indiv *child;
int findex;
int mindex;
int cindex;
int base;
} TRIO;
// ?index into original Indiv array. base is work variable used in phasetrio to store init index in new array
typedef struct
{
char gname[IDSIZE];
SNP **snpm;
Indiv **indivm;
int numsnps;
int numindivs;
int rlen;
int fdes;
int snpindex;
unsigned char *buff;
} genofile;
typedef struct
{
double xd[4];
double xc[9];
double ap1;
double ap2;
double cp1;
double cp2;
double rpowersum;
double crpowersum;
double gammasum[2];
double gammanum[2];
int pubfmodern;
} SNPMC;
// gammasum for cases/controls
#endif
#define ADMUTILS
void loadstats (FILE * statsfile, Indiv * indiv_array, int *numindivs);
void loadXstats (FILE * Xstatsfile, Indiv * indiv_array, int numindivs,
int *numloaded);
void sett1 (double *tt, double theta, int numstates);
void sett1r (double *tt, double theta, int numstate, double risks);
void gettln (SNP * cupt, Indiv * indx,
double *ptheta, double *plambda, int *pnumstates, int *pignore);
void puttln (SNP * cupt, Indiv * indx, double theta, double lambda);
/* UTILITY FUNCTIONS */
int countcol (char *fname);
int countcolumns (FILE * fp);
void fataly (const char *name);
int compare_doubles (const void *a, const void *b);
void pcheck (char *name, char x);
void printm (double **M, int numstates);
int numvalids (Indiv * indx, SNP ** snpmarkers, int fc, int lc);
void gethpos (int *fc, int *lc, SNP ** snpm, int numsnps,
int xchrom, int lo, int hi);
int numvalidgtypes (SNP * cupt);
double malefreq (Indiv ** indivmarkers, int numindivs);
int isimatch (int a, int b);
void makedir (char *dirname);
int indxindex (char **namelist, int len, char *strid);
int indindex (Indiv ** indivmarkers, int numindivs, char *indid);
int snpindex (SNP ** snpmarkers, int numsnps, char *snpid);
void inddupcheck (Indiv ** indivmarkers, int numindivs);
void freesnpindex ();
int ignoresnp (SNP * cupt);
double entrop (double *a, int n);
double xxlog2 (double t);
void testnan (double *a, int n);
void hap2dip (SNP * cupt);
void flipalleles (SNP * cupt);
void flipalleles_phased (SNP * cupt);
int getgtypes (SNP * cupt, int k);
void putgtypes (SNP * cupt, int k, int val);
int getep (SNP * cupt, int k);
void putep (SNP * cupt, int k, int val);
int hasharr (char **xarr, int nxarr);
void wbuff (unsigned char *buff, int num, int g);
int rbuff (unsigned char *buff, int num);
int ridfile (char *fname);
double hwcheck (SNP * cupt, double *cc);
double hwcheckx (SNP * cupt, Indiv ** indm, double *cc);
void cntit (double *xc, SNP * cupt1, SNP * cupt2);
int setid2pops (char *idpopstring, Indiv ** indmarkers, int numindivs) ;
// dup routines
void setfastdupnum (int num);
void setfastdupthresh (double thresh, double kill);
void killxhets (SNP ** snpmarkers, Indiv ** indivmarkers, int numsnps,
int numindivs);
void fastdupcheck (SNP ** snpmarkers, Indiv ** indivmarkers, int numsnps,
int numindivs);
int grabgtypes (int *gtypes, SNP * cupt, int numindivs);
int kcode (int *w, int len, int base);
void cdup (SNP ** snpm, Indiv ** indm, int nsnp, int *buff, int lbuff);
void printdup (SNP ** snpm, int nsnp, Indiv * inda, Indiv * indb, int nmatch,
int nnomatch);
void killdup (Indiv * inda, Indiv * indb, SNP ** snpm, int nsnp);
double kurtosis (double *a, int n);
int getlist (char *name, char **list);
void printvers (char *progname, char *vers);
int numvalidind (Indiv ** indivmarkers, int numind);
void numvalidgtallind (int *x, SNP ** snpm, int numsnps, int numind);
int numvalidgtind (SNP ** snpm, int numsnps, int ind);
int numvalidgt (Indiv ** indivmarkers, SNP * cupt);
int numvalidgtx (Indiv ** indivmarkers, SNP * cupt, int affst);
int isxmale (SNP * cupt, Indiv * indx);
void printmatz (double *ww, char **eglist, int n);
void printmatz5 (double *ww, char **eglist, int n);
void printmatz10 (double *ww, char **eglist, int n);
char *get3 (char *ss);
char *getshort (char *ss, int n);
#undef max
#define max(A,B) ((A) > (B) ? (A) : (B))
#define MAXNUMR 200
// max number models
#define CNULL '\0'
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