#include <stdio.h>
#include <stdlib.h>
#include <htslib/sam.h>

using namespace std; 

#define bam_is_read1(b) (((b)->core.flag&BAM_FREAD1) != 0)

uint8_t Base[16] = {0,65,67,0,71,0,0,0,84,0,0,0,0,0,0,78};

int main(int argc, char **argv)
{
 bam_hdr_t *header;
 bam1_t *aln = bam_init1();

 samFile *in = sam_open(argv[1], "r");
 htsFile *outR1 = hts_open(argv[2], "wb");
 header = sam_hdr_read(in);
 if (sam_hdr_write(outR1, header) < 0) {
 fprintf(stderr, "Error writing output.\n");
 exit(-1);
 }
 uint8_t *seq;
 int32_t lseq;
 uint32_t *cigar;
 char* qname;
 while (sam_read1(in, header, aln) >= 0) {
 if (bam_is_read1(aln)){
  sam_write1(outR1, header, aln);
 }
 else {
  seq = bam_get_seq(aln);
  lseq = aln->core.l_qseq;
  qname = bam_get_qname(aln);
  printf("%s\n",qname);
  cigar = bam_get_cigar(aln);
  for(int i=0; i < aln->core.n_cigar;++i){
  int icigar = cigar[i];
  printf("%d%d\n",bam_cigar_op(icigar),bam_cigar_oplen(icigar));
  }
  for(int i=0; i < lseq;++i){
  printf("%c", Base[bam_seqi(seq, i)]);
  }
  printf("\n");

 }
 }
 sam_close(in);
 sam_close(outR1);
}