adaptive-pulldown/popsubs.h at master · DReichLab/adaptive-pulldown · GitHub

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#include "nicksam.h"
#include "ultima.h"

#define MAXFF 100
#define SSIZE 50
#define MAXFPOPS 5000
#define HUGELEN  10000

extern int verbose ;
void printbadrgs()  ;
void freebonetable()  ;
int loadbonetable(char *bfname)  ;
int loadstr(char **strlist, char **xlist, int numin) ;
int bone2num(char *ss) ;
int library2num(char *ss) ;
int crackhdr(char *hdr, char *lib, char *samp, char *pop) ;
int getbone(char *library, char *bone, char *hdr, char *bonefile) ;
int getxstr(char ***xx, int maxrow, int numcol, char *fname) ;
int indxsub(char *ss, char **table, int tablen) ;
int check(char *sa, char *sb) ;
char *popstring(char **popl, int n) ; // first character
void setoldtags() ;

void loadfilebase(char *parname) ;
void unloadfilebase() ;

void freerdtable()  ;
int loadrdtable(char *rdname)  ;
int whichhdr(char *s1) ;
int whichlib(char *s1) ;
int whichpop(char *s1) ;
void fixrgstring(char *rgs) ;
int checkrg(char **rawp) ;
int oldwhichpop(char *s1, char *lib, char *samp, char *pop) ;


int base2num(char c) ;
char num2base(int k) ;
int kodex (int *aa, int len)  ;
int kode4 (int *aa)  ;
void setqhack(int val) ;
void dekodex (int kode, int *aa, int len)  ;
void dekode4 (int kode, int *aa)  ;
int kodexb (int *aa, int len, int base)  ;
int setpmdscore(int val) ;
void dekodexb (int kode, int *aa, int len, int base)  ;
char *binary_string(int a, int len) ;
void printmat0(double *a, int m, int n) ;
void loadbaseprobs(double **basep, int *basevalid, PILEUP *pilept, int rind) ;
char *getfaname(char *sname) ;
int patkode(int a, int b, int c, int d) ;
char *kodepstring(int kode) ;
int checkag(int *aa, int len) ;
int abpat(int *ww, int *aa, int len, int rind) ;
int setrdtable(char **plist, int nplist, char *rdname) ;
int loadbadbonelist(char *badlist)   ;
int  loadlist(char **list, char *listname)   ;
char *num2h(int k) ;
int abx(int a, int b) ;
int abxok(int abx, int abxmode) ;
char *abxstring(int abx) ;

int isold(char *pop) ;
int isdenisova(char *pop) ;
int isneandertal(char *pop) ;
void setancient(READ *readpt) ;

int calcvar(PILEUP *pilept, int *vnum, int nean) ;
void cntalleles(PILEUP *pilept, int *ccc) ;
void cntallelesnonean(PILEUP *pilept, int *ccc, int nean) ;
void forcebi(PILEUP *pilept, int xa, int xb) ;
void copybb(BASEP *basept, int a, int b) ;
int calcvind(int *ccc, int rind, int *pvind) ;
int checkicx(int *ccc, int rind, int *pvind) ;
int checktri(int *ccc, int rind) ;

int getreadx(READ *readpt, char *line) ;
int getreadf(READ *readpt, FILE *fff) ;
int getreadfnorg(READ *readpt, FILE *fff) ;
int getread(READ *readpt) ;
int calcnumposdiff(READ *readpt) ;
void cleanread(READ *readpt) ;
void loadqinfo(char *qinfoname, double qnean) ;
void printqinfo() ;
int goodqualp(READ *readpt, int i, THRESH *pthresh)  ;
int goodqual(READ *readpt, int i)  ;
int is_mono(int *aa, int len)  ;
int is_biallelic(int *aa, int len)  ;
void mkqual(int *iqual, char *qual, int len) ;
void getpophdr(char **pophdr, char **poplist, int npops) ;
int getfastalist(char **poplist, int npops, char *dbfile, char **rglist, int *rgpops)  ;
int getrg(char **poplist, int npops, char *dbfile, char **rglist, int *rgpops)  ;
int getrgj(char **rawpoplist, int npops, char *dbfile, char **rglist, int *rgpops) ;
void printrghit()  ;
int mkfullpoplist(char **fullpoplist, int *f2pops, char **rawpoplist, int npops) ;
int countg(char *uu, int nuu, int snpref, int snpvar)  ;
int countc(char *uu, int nuu, char var, char ref)  ;
void printread(READ *readpt) ;
int grabreference(char *reg, int pos, int len, char *refstring)  ;
void getnumreads(long *plong, long *ptotal)  ;
void makergcats(char *rrr, char *bamname)  ;
char xrefbase(int pos, char *regstring, int reglen) ;
void writefaf(FILE *fff, char *regname, char *rrr)  ;
int getrgcat(int *rgcats, char **rgclist, int numrgc, char *rggroup) ;
int qcpg1(int pos, char *regstring, int reglen ) ;
int qcpg2(int pos, char *regstring, int reglen, char ca, char cb) ;
int atop(int a, int nump)  ;
int ptoa(int p, int nump)  ;
int split1rx (char *strin, char *strpt[], char splitc, char stopc) ;
void mkfname2(char *fname2, char *fname) ;
void printhistx(int ultmode) ;
int fixindels(READ *rpt, READ *rptx)  ;
void fixbase(READ *readpt, int winlen)  ;

char *getfaiub(int k) ;
int isloshlass(char *pop) ;
void setrcstrip(int mode) ;
void  setthreshx(THRESH *pthresh)  ;
void  cleanthresh(THRESH *pthresh) ;
int flnum(READ *readpt, char *rstring, int rlen, char *polystring, int polylen, int *xf, int *xl)  ;

#ifndef NJPQINFO
typedef struct {
 char popname [15] ;
 int popind ;
 int chimpbasenum ;
 int strand ;
 int loqual ;
 int hiqual ;
 double loprob ;
} QINFO ;

// specifies loqual and hiqual for pop given chimp base
// refinement if qual = loqual base only accepted with probability loprob

#endif
#define NJPQINFO

#ifndef _POPDEF_
#define _POPDEF_


#endif