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/*
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* Fasta.hpp
*
* Created on: May 27, 2009
* Author: caa
*/
#ifndef FASTA_HPP_
#define FASTA_HPP_
#include <string>
#include "bam.h"
#include "faidx.h"
namespace fasta {
using namespace std;
class Fasta {
public:
Fasta()
{
fai=NULL;
}
Fasta(const string & fileName)
{
fai=NULL;
fai = fai_load(fileName.c_str());
if (!fai) {
throw string("Fasta: cannot open reference file.");
}
}
string getSequence(const string & tid, int start, int end)
{
char *str;
char *ref;
str = (char*)calloc(strlen(tid.c_str()) + 30, 1);
sprintf(str, "%s:%d-%d", tid.c_str(), start, end);
int len;
ref = fai_fetch(fai, str, &len);
if (len==0) throw string("faidx error, len==0");
string result(ref);
transform(result.begin(), result.end(), result.begin(), ::toupper);
free(str);
free(ref);
return result;
}
~Fasta()
{
if (fai) fai_destroy(fai);
}
protected:
faidx_t *fai;
};
}
#endif /* FASTA_HPP_ */
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