int main (int *argc, char **argv) {
char *tab;
char *accession;
SRAMgr const *sra;
SRATable const *tbl;
spotid_t nspots;
rc_t rc;
tab = argv[1];
accession = argv[2];
rc = openTable(tab, &sra, &tbl, &nspots);
if (rc != 0) {
return rc;
}
printf("There are %d spots\n", nspots);
// rc = getReads(tbl, accession, 10);
rc = getBases(tbl, 1, 10);
if (rc != 0) {
closeTable(sra, tbl);
return 1;
}
printf("\n");
rc = getQuals(tbl, 1, 10);
if (rc != 0) {
closeTable(sra, tbl);
return 1;
}
getInfo(tbl, 1, 10);
getRanges(tbl);
closeTable(sra, tbl);
return 0;
}
void printReadBuffered(aRead &rd,aHead *hd,kstring_t &str) {
str.l = 0;
if(bam_validate1(hd,rd)==0){
fprintf(stderr,"problems validateing\n");
exit(0);
}
kputsn((char *)rd.vDat,rd.l_qname-1,&str);kputc('\t', &str);
kputw((int)rd.flag_nc>>16, &str); kputc('\t', &str);
if(rd.refID==-1)//unmatched read
kputc('*', &str);
else
kputs(hd->name[rd.refID] , &str);
kputc('\t', &str);
kputw(rd.pos+1, &str); kputc('\t', &str);
kputw(rd.mapQ, &str);kputc('\t', &str);
int nCigs = rd.nCig;
if(nCigs==0)
kputc('*', &str);// if no cigars
else{
for (int i = 0; i < nCigs; ++i) {//print cigars
uint32_t *cigs =getCig(&rd);
kputw(cigs[i]>>BAM_CIGAR_SHIFT, &str);
kputc("MIDNSHP"[cigs[i]&BAM_CIGAR_MASK], &str);
}
}
kputc('\t', &str);
if(rd.next_refID==-1)
kputc('*', &str);// if no cigars
else if(rd.refID==rd.next_refID)
kputc('=', &str);
else
kputs(hd->name[rd.next_refID] , &str);
kputc('\t', &str);
kputw(rd.next_pos+1, &str); kputc('\t', &str);
kputw(rd.tlen, &str); kputc('\t', &str);
//start seq
char *seq = (char *)getSeq(&rd);
for(int i=0;i<rd.l_seq;i++)
kputc(bam_nt16_rev_table2[bam1_seqi(seq, i)], &str);
kputc('\t', &str);
char *quals =(char *)getQuals(&rd);
for(int i=0;i<rd.l_seq;i++)
kputc(quals[i]+33, &str);
//below is taken directly from samtools,(not to steal, to preserve ordering etc, all credits go where credit is due)
//from aux start to the last memadrs in chunk
printAuxBuffered(getAuxStart(&rd),rd.vDat+rd.block_size,str);
kputc('\n', &str);
}