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lib/Bio/DB/Sam.xs  view on Meta::CPAN

   str[strlen(str)-1] = '\0';
   RETVAL = str;
OUTPUT:
   RETVAL

SV*
bama_aux_get(b,tag)
   Bio::DB::Bam::Alignment b
   char*               tag
PROTOTYPE: $$
PREINIT:
   int           type;
   uint8_t       *s;
CODE:
   s    = bam_aux_get_core(b,tag);
   if (s==0)
      XSRETURN_EMPTY;
   type = *s++;
   switch (type) {
   case 'c':
     RETVAL = newSViv((int32_t)*(int8_t*)s);
     break;
   case 'C':
     RETVAL = newSViv((int32_t)*(uint8_t*)s);
     break;
   case 's':
     RETVAL = newSViv((int32_t)*(int16_t*)s);
     break;
   case 'S':
     RETVAL = newSViv((int32_t)*(uint16_t*)s);
     break;
   case 'i':
     RETVAL = newSViv(*(int32_t*)s);
     break;
   case 'I':
     RETVAL = newSViv((int32_t)*(uint32_t*)s);
     break;
   case 'f':
     RETVAL = newSVnv(*(float*)s);
     break;
   case 'Z':
   case 'H':
     RETVAL = newSVpv((char*)s,0);
     break;
   case 'A':
     RETVAL = newSVpv((char*)s,1);
     break;
   default:
     XSRETURN_EMPTY;
   }
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; }
       else if (type == 's') { s += 2; }
       else if (type == 'I') { s += 4; }
       else if (type == 'i') { s += 4; }
       else if (type == 'f') { s += 4; }
       else if (type == 'Z' || type == 'H') { while (*s) ++(s); ++(s); }
     }
   }

SV*
bama_data(b,...)
    Bio::DB::Bam::Alignment b
PROTOTYPE: $;$
PREINIT:
    STRLEN  len;
CODE:
    if (items > 1) {
      b->data     = SvPV(ST(1),len);
      b->data_len = len;
    }
    RETVAL=newSVpv(b->data,b->data_len);
OUTPUT:
    RETVAL

int
bama_data_len(b,...)
    Bio::DB::Bam::Alignment b
PROTOTYPE: $;$
CODE:
    if (items > 1)
      b->data_len = SvIV(ST(1));
    RETVAL=b->data_len;
OUTPUT:
    RETVAL

int
bama_m_data(b,...)
    Bio::DB::Bam::Alignment b
PROTOTYPE: $;$
CODE:
    if (items > 1) {
      b->m_data = SvIV(ST(1));
    }
    RETVAL=b->m_data;
OUTPUT:
    RETVAL

SV*
bama_qname(b)
  Bio::DB::Bam::Alignment b
PROTOTYPE: $

lib/Bio/DB/Sam.xs  view on Meta::CPAN

  PROTOTYPE: $
  CODE:
    RETVAL = bamh->n_targets;
  OUTPUT:
    RETVAL

SV*
bam_target_name(bamh)
  Bio::DB::Bam::Header bamh
  PROTOTYPE: $
  PREINIT:
    int i;
    AV * avref;
  CODE:
    avref = (AV*) sv_2mortal((SV*)newAV());
    for (i=0;i<bamh->n_targets;i++)
      av_push(avref, newSVpv(bamh->target_name[i],0));
    RETVAL = (SV*) newRV((SV*)avref); 
  OUTPUT:
    RETVAL

SV*
bam_target_len(bamh)
    Bio::DB::Bam::Header bamh
  PROTOTYPE: $
  PREINIT:
    int i;
    AV * avref;
  CODE:
    avref = (AV*) sv_2mortal((SV*)newAV());
    for (i=0;i<bamh->n_targets;i++)
       av_push(avref, newSViv(bamh->target_len[i]));
    RETVAL = (SV*) newRV((SV*)avref); 
  OUTPUT:
    RETVAL

SV*
bam_text(bamh, ...)
  Bio::DB::Bam::Header bamh
  PREINIT:
    char   *newtext;
    STRLEN n;
  CODE:
    /* in case text is not null terminated, we copy it */
    RETVAL = newSVpv(bamh->text,bamh->l_text);
    if (items > 1) {
      newtext = (char*) SvPV(ST(1),n);
      strcpy(bamh->text,newtext);
      bamh->l_text = n;
    }
  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);
	PUSHs(sv_2mortal(newSViv(seqid)));
	PUSHs(sv_2mortal(newSViv(start)));
	PUSHs(sv_2mortal(newSViv(end)));
      }
    }

void
bam_view1(bamh,alignment)
     Bio::DB::Bam::Header     bamh
     Bio::DB::Bam::Alignment  alignment
     PROTOTYPE: $$
     CODE:
       bam_view1(bamh,alignment);

void
bam_DESTROY(bamh)
  Bio::DB::Bam::Header bamh
  PROTOTYPE: $
  CODE:
    bam_header_destroy(bamh);

MODULE = Bio::DB::Sam PACKAGE = Bio::DB::Bam::Index PREFIX=bami_

int
bami_fetch(bai,bfp,ref,start,end,callback,callbackdata=&PL_sv_undef)
  Bio::DB::Bam::Index bai
  Bio::DB::Bam        bfp
  int   ref
  int   start
  int   end
  CV*   callback
  SV*   callbackdata
PREINIT:
  fetch_callback_data fcd;
CODE:
  {
    fcd.callback = (SV*) callback;
    fcd.data     = callbackdata;
    RETVAL = bam_fetch(bfp,bai,ref,start,end,&fcd,bam_fetch_fun);
  }
OUTPUT:
    RETVAL

void
bami_lpileup(bai,bfp,ref,start,end,callback,callbackdata=&PL_sv_undef)
  Bio::DB::Bam::Index bai
  Bio::DB::Bam        bfp
  int   ref
  int   start
  int   end