int bammer_main(args *pars){
gf=(getFasta *) allMethods[1];
func = pars->callback;
std::vector<char *> nams;
//read bamfiles
if(pars->inputfiles)
nams = angsd::getFilenames(pars->inputfiles,pars->nInd);
else
nams.push_back(strdup(pars->inputfile));//if only one file just push bamfile
bufReader *rd = initializeBufReaders2(nams);
//read regions
std::vector<char *> regionsRaw;
if(pars->regionfile)
regionsRaw = getRegions(pars->regionfile);
else if(pars->region!=NULL){
regionsRaw.push_back(strdup(pars->region));//if only one file just push bamfile
}
std::vector<regs> regions;
for(size_t i=0;i<regionsRaw.size();i++){
regs tmpRegs;
if(parse_region(regionsRaw[i],*rd[0].hd,tmpRegs.refID,tmpRegs.start,tmpRegs.stop)<0||tmpRegs.stop<tmpRegs.start){
fprintf(stderr,"[%s] problems with indexing: %s\n",__FUNCTION__,regionsRaw[i]);
exit(0);
}else
regions.push_back(tmpRegs);
}
//printReg(stderr,regions)
//each filereader contains a filename for a bam, if we try to read remote files, then we need to download the bai file, and update the filename
if(regions.size()!=0)
modNames(rd,nams.size());
extern int maxThreads;
if(pars->jobtype==2)
uppile(pars->show,maxThreads,rd,pars->nLines,nams.size(),regions);
else if(pars->jobtype==1)
while(motherView(rd,nams.size(),regions));
else{
fprintf(stderr,"nothing to do? what should program do?\n");
}
//cleanup stuff
for(int i=0;i<(int)nams.size();i++){
free(nams[i]);
dalloc_bufReader(rd[i]);
}
for(size_t i=0;i<regions.size();i++)
free(regionsRaw[i]);
delete [] rd;
free(pars->inputfiles);free(pars->inputfile);free(pars->region);
delete pars;
return 0;
}
int bammer_main(argStruct *args){
gf=(abcGetFasta *) allMethods[1];
//read bamfiles
extern int checkBamHeaders;
bufReader *rd = initializeBufReaders2(args->nams,checkBamHeaders);
extern int maxThreads;
uppile(args->show,maxThreads,rd,args->nLines,args->nams.size(),args->regions,gf);
//cleanup stuff
for(unsigned i=0;i<args->nams.size();i++)
dalloc_bufReader(rd[i]);
delete [] rd;
return 0;
}
