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/*
* Copyright [2015-2018] EMBL-European Bioinformatics Institute
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include "EXTERN.h"
#include "perl.h"
#include "XSUB.h"
#include <stdio.h>
#include <string.h>
#include "htslib/faidx.h"
#ifndef Newx
# define Newx(v,n,t) New(0,v,n,t)
#endif
// Code is written to use a blessed int pointer to this strut as an object
// You cannot use Data::Dumper to inspect the Faidx object. Sorry
typedef struct
{
char* path;
faidx_t* index;
} Faidx ;
SV* new(const char * classname, const char * path)
{
Faidx * faidx;
SV * obj;
SV * obj_ref;
faidx_t * fai;
Newx(faidx, 1, Faidx);
fai = fai_load(path);
faidx->path = savepv(path);
faidx->index = fai;
obj = newSViv((IV)faidx);
obj_ref = newRV_noinc(obj);
sv_bless(obj_ref, gv_stashpv(classname, GV_ADD));
SvREADONLY_on(obj);
return obj_ref;
}
void get_sequence(SV* obj, SV* location, SV** seq, int* seq_len)
{
faidx_t *fai;
char* char_seq;
*seq = newSVpvn("",0);
*seq_len = 0;
fai = ((Faidx*)SvIV(SvRV(obj)))->index;
//Fetch sequence
char_seq = fai_fetch(fai, SvPV(location, PL_na), seq_len);
//Push into a SV
sv_catpv(*seq, char_seq);
sv_2mortal(*seq);
//Free the buffer created by faidx
free(char_seq);
}
void get_sequence2(SV* obj, SV* seq_id, int start, int end, SV** seq, int* seq_len)
{
faidx_t *fai;
char* char_seq;
*seq = newSVpvn("",0);
*seq_len = 0;
fai = ((Faidx*)SvIV(SvRV(obj)))->index;
//Fetch sequence
char_seq = faidx_fetch_seq(fai, SvPV(seq_id, PL_na), start, end, seq_len);
//Push into a SV
sv_catpv(*seq, char_seq);
sv_2mortal(*seq);
//Free the buffer created by faidx
free(char_seq);
}
int has_sequence(SV* obj, SV* seq_id)
{
int has_seq=-1 ;
has_seq = faidx_has_seq(((Faidx*)SvIV(SvRV(obj)))->index, SvPV(seq_id, PL_na));
return has_seq;
}
int length(SV* obj, char* seq_id)
{
int length = 0 ;
faidx_t *fai = ((Faidx*)SvIV(SvRV(obj)))->index ;
length = faidx_seq_len(fai, seq_id) ;
return length ;
}
void DESTROY(SV* obj)
{
Faidx* faidx = (Faidx*)SvIV(SvRV(obj));
Safefree(faidx->path);
fai_destroy(faidx->index);
Safefree(faidx);
}
MODULE = Bio::DB::HTS::Faidx PACKAGE = Bio::DB::HTS::Faidx
PROTOTYPES: ENABLE
SV*
new(classname, path)
char* classname
char* path
void
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
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