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lib/Bio/DB/Sam.xs  view on Meta::CPAN

OUTPUT:
   RETVAL

void
bama_aux_keys(b)
Bio::DB::Bam::Alignment b
PROTOTYPE: $
PREINIT:
   uint8_t *s;
   uint8_t type;
PPCODE:
   {
     s = bam1_aux(b);  /* s is a khash macro */
     while (s < b->data + b->data_len) {
       XPUSHs(sv_2mortal(newSVpv(s,2)));
       s   += 2; 
       type = *s++;
       if      (type == 'A') { ++s; }
       else if (type == 'C') { ++s; }
       else if (type == 'c') { ++s; }
       else if (type == 'S') { s += 2; }

lib/Bio/DB/Sam.xs  view on Meta::CPAN

  OUTPUT:
    RETVAL

void
bam_parse_region(bamh,region)
    Bio::DB::Bam::Header bamh
    char*            region
    PROTOTYPE: $
    PREINIT:
       int seqid,start,end;
    PPCODE:
    {
      bam_parse_region(bamh,
		       region,
		       &seqid,
		       &start,
		       &end);
      if (seqid < 0)
	XSRETURN_EMPTY;
      else {
	EXTEND(sp,3);