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abcGL.h
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abcGL.h
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#include "soap_likes.h"
#include "gatk_likes.h"
#include "bam_likes.h"
#include "simple_likes.h"
#include "ancestral_likes.h"
class abcGL:public abc{
private:
BGZF *outfileSAF;
FILE *outfileSAFIDX;
BGZF *outfileSAFPOS;
const char * postfix;
const char * beaglepostfix;
//below is for SYK
double **errors;
char * errorFname;
double ****errorProbs;
//below is used for output
kstring_t bufstr;
//soap method is implemented as a class
soap_likes soap;
// ancestral method is implemented as a class
anc_likes ancestral_lik;
//a tempdir used by SOAPsnp for the recalibration matrices
char *angsd_tmpdir;
//below used for filtering qscore,mapQ and trimming
int trim;
int64_t offs[2];
BGZF *gzoutfile;
BGZF *gzoutfile2;
int GL;
int doGlf;
int minInd;
char *tmpChr;
int nnnSites;
void getLikesFullError10Genotypes(int numSites,int nInd,suint **counts,double ****errorProbs,int *keepSites,double **loglikes);
void printLike(funkyPars *pars);
public:
void run(funkyPars *pars);
void print(funkyPars *pars);
void clean(funkyPars *pars);
void getOptions(argStruct *arguments);
void printArg(FILE *argFile);
void changeChr(int refId);
abcGL(const char *outfiles,argStruct *arguments,int inputtype);
~abcGL();
};