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lib/Bio/DB/HTS/Faidx.xs  view on Meta::CPAN

get_sequence(obj, location, OUTLIST seq, OUTLIST length)
  SV* obj
  SV* location
  SV* seq
  int length = NO_INIT
  CODE:
     get_sequence(obj, location, &seq, &length) ;


void
get_sequence_no_length(obj, location, OUTLIST seq)
  SV* obj
  SV* location
  SV* seq
CODE:
  int seq_len=0 ;
  get_sequence(obj, location, &seq, &seq_len) ;


void
get_sequence2(obj, seq_id, start, end, OUTLIST seq, OUTLIST length)
  SV* obj
  SV* seq_id
  int start
  int end
  SV* seq
  int length = NO_INIT


void
get_sequence2_no_length(obj, seq_id, start, end, OUTLIST seq)
  SV* obj
  SV* seq_id
  int start
  int end
  SV* seq
CODE:
  int seq_len=0 ;
  get_sequence2(obj, seq_id, start, end, &seq, &seq_len) ;


int
has_sequence(obj, seq_id)
  SV* obj
  SV* seq_id


int
length(obj, seq_id)
  SV* obj
  char* seq_id


void
get_all_sequence_ids(obj)
   SV* obj
INIT:
   int num_seqs ;
   int i ;
    const char* faidx_name ;
PPCODE:
    num_seqs = 0 ;
    faidx_t *fai = ((Faidx*)SvIV(SvRV(obj)))->index ;
    num_seqs = faidx_nseq(fai) ;
    EXTEND(SP,num_seqs);
    for( i=0 ; i<num_seqs ; i++ )
    {
      faidx_name = faidx_iseq(fai,i) ;
      PUSHs(sv_2mortal(newSVpv(faidx_name,0))) ;
    }


void
DESTROY(obj)
  SV* obj