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/*Copyright (C) 2015 Olivier Delaneau, Halit Ongen, Emmanouil T. Dermitzakis
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/>.*/
#ifndef _COMPRESSED_IO_H
#define _COMPRESSED_IO_H
//STL INCLUDES
#include <iostream>
#include <sstream>
#include <fstream>
//BOOST INCLUDES
#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/filter/gzip.hpp>
#include <boost/iostreams/filter/bzip2.hpp>
class input_file : public boost::iostreams::filtering_istream {
protected:
ifstream file_descriptor;
public:
input_file(string filename) {
if (filename.substr(filename.find_last_of(".") + 1) == "gz") {
file_descriptor.open(filename.c_str(), ios::in | ios::binary);
push(boost::iostreams::gzip_decompressor());
} else if (filename.substr(filename.find_last_of(".") + 1) == "bz2") {
file_descriptor.open(filename.c_str(), ios::in | ios::binary);
push(boost::iostreams::bzip2_decompressor());
} else file_descriptor.open(filename.c_str());
if (!file_descriptor.fail()) push(file_descriptor);
}
~input_file() {
close();
}
bool fail() {
return file_descriptor.fail();
}
void close() {
if (!file_descriptor.fail()) {
if (!empty()) reset();
file_descriptor.close();
}
}
};
class output_file : public boost::iostreams::filtering_ostream {
protected:
ofstream file_descriptor;
public:
output_file(string filename) {
if (filename.substr(filename.find_last_of(".") + 1) == "gz") {
file_descriptor.open(filename.c_str(), ios::out | ios::binary);
push(boost::iostreams::gzip_compressor());
} else if (filename.substr(filename.find_last_of(".") + 1) == "bz2") {
file_descriptor.open(filename.c_str(), ios::out | ios::binary);
push(boost::iostreams::bzip2_compressor());
} else file_descriptor.open(filename.c_str());
if (!file_descriptor.fail()) push(file_descriptor);
}
~output_file() {
close();
}
bool fail() {
return file_descriptor.fail();
}
void close() {
if (!file_descriptor.fail()) {
if (!empty()) reset();
file_descriptor.close();
}
}
};
#endif
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