void abcFilter::getOptions(argStruct *arguments){
fname=angsd::getArg("-sites",fname,arguments);
if(fname!=NULL)
fl = filt_read(fname);
if(fl!=NULL)
fprintf(stderr,"\t-> [%s] -sites is still beta, use at own risk...\n",__FILE__);
//1=bim 2=keep
doMajorMinor = angsd::getArg("-doMajorMinor",doMajorMinor,arguments);
if(doMajorMinor==3 && fl!=NULL&& fl->hasExtra!=1){
fprintf(stderr,"\t-> Must supply -sites with a file containing major and minor if -doMajorMinor 3\n");
}
if(doMajorMinor!=3 && fl!=NULL&& fl->hasExtra==1){
fprintf(stderr,"\t-> Filter file contains major/minor information to use these in analysis supper \'-doMajorMinor 3\'\n");
}
capDepth = angsd::getArg("-capDepth",capDepth,arguments);
minInd = angsd::getArg("-minInd",minInd,arguments);
setMinIndDepth = angsd::getArg("-setMinDepthInd",setMinIndDepth,arguments);
strict = angsd::getArg("-strict",strict,arguments);
if(minInd >arguments->nInd){
fprintf(stderr,"\t-> Potential problem you filter -minInd %d but you only have %d samples?\n",minInd,arguments->nInd);
exit(0);
}
}
int main_sites(int argc,char **argv){
#if 0
for(int i=0;i<argc;i++)
fprintf(stderr,"argv[%d]:%s\n",i,argv[i]);
#endif
if(argc==1){
fprintf(stderr,"\tsites print filename\t\tPrint index file\n\tsites index filename [-r offset -compl doCompl]\tgenerate binary index file\n");
return 0;
}
--argc;++argv;
if(!strcasecmp(*argv,"index")){
filt_init(--argc,++argv);
}else if(!strcasecmp(*argv,"print")){
filt *f = filt_read(*++argv);
filt_print(stdout,f,NULL);
dalloc(f);
}else
fprintf(stderr,"Unknown option: \'%s\'\n",*argv);
return 0;
}
