int main(int argc, char** argv){
if(strcmp(ZLIB_VERSION,zlib_version)){
fprintf(stderr,"\t-> Problem with difference in zlib version used for compiling and linking\n");
fprintf(stderr,"\t-> ZLIB_VERSION: %s zlibversion: %s \n",ZLIB_VERSION,zlib_version);
//return 0;
}
fprintf(stderr,"\t-> angsd version: %s (htslib: %s) build(%s %s)\n",ANGSD_VERSION,hts_version(),__DATE__,__TIME__);
//no arguments supplied -> print info
if(argc==1||(argc==2&&(strcasecmp(argv[1],"--version")==0||strcasecmp(argv[1],"--help")==0))){//if haven't been supplied with arguments, load default,print, and exit
printProgInfo(stderr);
return 0;
}
if(!strcasecmp("sites",argv[1])){
//from prep_sites.* used for indexing -sites files
int main_sites(int argc,char **argv);
main_sites(--argc,++argv);
return 0;
}
//print time
clock_t t=clock();
time_t t2=time(NULL);
//intialize our signal handler for ctrl+c
catchkill();
argStruct *args=NULL;
if(argc==2){
fprintf(stderr,"\t-> Analysis helpbox/synopsis information:\n");
multiReader mr(argc,argv);
args = mr.getargs();
init(args);//program dies here after printing info, if a match is found
fprintf(stderr,"\nUnknown argument supplied: \'%s\'\n\n",argv[1]);
printProgInfo(stderr);
exit(0);//important otherwise the abc classes will try to clean up, which doesnt make sense in this context
// return 0;
}
multiReader *mr= new multiReader(argc,argv);
args = mr->getargs();
init(args);
// fprintf(stderr,"adsfadsf\n");exit(0);
parseArgStruct(args);
//Below is main loop which will run until nomore data
assert(args->hd);
assert(args->revMap);
int lastRefId=-1;
while(SIG_COND) {
funkyPars *tmp = mr->fetch(); //YES MISTER FETCH
if(tmp==NULL)
break;
if(lastRefId==-1||lastRefId!=tmp->refId){
lastRefId=tmp->refId;
void changeChr(int refId);//<-ugly is located in shared.cpp, to force a change of chr, when notusing bamfiles
changeChr(lastRefId);
}
selector(tmp);
}
//now we have no more data lets wait and cleanup
fprintf(stderr,"\t-> Done reading data waiting for calculations to finish\n");
destroy_shared();
//printout the filenames generated
fprintf(stderr,"\t-> Output filenames:\n");
for(int i=0;i<(int)dumpedFiles.size();i++){
fprintf(stderr,"\t\t->\"%s\"\n",dumpedFiles[i]);
fprintf(args->argumentFile,"\t\t->\"%s\"\n",dumpedFiles[i]);
free(dumpedFiles[i]);
}
// fprintf(stderr,"\n");
fprintf(args->argumentFile,"\n");
// fprintf(stderr,"\t");
printTime(stderr);
//print out nice messages
fprintf(stderr,"\t-> Arguments and parameters for all analysis are located in .arg file\n");
fprintf(stderr, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(stderr, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
fprintf(args->argumentFile, "\t[ALL done] cpu-time used = %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
fprintf(args->argumentFile, "\t[ALL done] walltime used = %.2f sec\n", (float)(time(NULL) - t2));
//make better below
extern int *bamSortedIds;
delete [] bamSortedIds;
delete mr;
return 0;
}
int main(int argc,char**argv){
main_sites(--argc,++argv);
}
