bufReader initBufReader2(const char*fname,int doCheck,char *fai_fname){
bufReader ret;
ret.fn = strdup(fname);
int newlen=strlen(fname);//<-just to avoid valgrind -O3 uninitialized warning
ret.fp = openBAM(ret.fn,doCheck);
if (fai_fname && hts_set_fai_filename(ret.fp, fai_fname) != 0) {
fprintf(stderr, "[%s] failed to process %s\n",
__func__, fai_fname);
exit(EXIT_FAILURE);
}
ret.isEOF =0;
ret.itr=NULL;
ret.idx=NULL;
ret.hdr = sam_hdr_read(ret.fp);
if(strlen(ret.hdr->text)==0){
fprintf(stderr,"\t-> No header information could be found for BAM/CRAM file: \'%s\' will exit\n",fname);
exit(1);
}
checkIfSorted(ret.hdr->text);
if(ret.hdr==NULL) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", ret.fn);
exit(0);
}
return ret;
}
bufReader initBufReader2(const char*fname){
bufReader ret;
ret.bamfname = strdup(fname);
ret.fp = openBAM(ret.bamfname);
ret.hd = getHd(ret.fp);
ret.isEOF =0;
ret.it.from_first=1;//iterator, used when supplying regions
ret.it.finished=0;//iterator, used when supplying regions
ret.it.off = NULL;
ret.it.dasIndex = NULL;
return ret;
}
bufReader initBufReader2(const char*fname){
bufReader ret;
ret.fn = strdup(fname);
int newlen=strlen(fname);//<-just to avoid valgrind -O3 uninitialized warning
ret.fp = openBAM(ret.fn);
ret.isEOF =0;
ret.itr=NULL;
ret.idx=NULL;
ret.hdr = sam_hdr_read(ret.fp);
if(ret.hdr==NULL) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", ret.fn);
exit(0);
}
return ret;
}
