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/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA 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 Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent No laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikal Salson mikael.salson@lifl.fr
Hlne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/*
* file: izlib.hpp
* created: Feb 22, 2018 Thu
*/
#pragma once
#include <vector>
#include "zlib.h"
#define SIZE_32 32768U /* buffer size 32M */
#define SIZE_16 16384U /* buffer size 16M */
#define RL_OK 0
#define RL_END 1
#define RL_ERR -1
class Izlib
{
public:
Izlib(bool is_compress=false, bool is_init=true);
void init(bool is_compress = false);
int reset_deflate(); // clean up z_stream
int finish_deflate(std::ostream& ofs, const int&& dbg=0);
int reset_inflate();
/*
* get a line from the compressed stream
*
* TODO: Make sure the stream is OK before calling this function.
* std::getline doesn't return error if the stream is not
* readable/closed. It returns the same input it was passed.
* @param ifs IN stream to get data from
* @param line IN/OUT line to populate
* @return RL_OK (0) | RL_END (1) | RL_ERR (-1)
*/
int getline(std::ifstream& ifs, std::string& line);
/*
* deflate passed string and append it to the file stream. Finish processing when the string has 0 size
* prototype: https://github.com/madler/zlib/blob/master/examples/zpipe.c:def
*
* @param readstr a Read as string to be compressed. String of 0 size indicates the end of processing.
* @param ofs compressed output file stream
* @param is_last flags the last string passed -> Finish compressing
* @return execution status
*/
int defstr(const std::string& readstr, std::ostream& ofs, bool is_last=false, const int&& dbg=0);
private:
char* line_start; // pointer to the start of a line within the 'z_out' buffer
z_stream strm; // stream control structure. Holds stream in/out buffers (byte arrays), sizes, positions etc.
size_t buf_in_size;
size_t buf_out_size;
unsigned z_in_num; // number of reads accumulated in IN buffer. For debugging.
std::vector<unsigned char> z_in; // IN buffer
std::vector<unsigned char> z_out; // OUT buffer
private:
/*
* inflate data until EOF or (OUT buffer is full) or (OUT buffer not full + IN buffer empty)
*/
int inflatez(std::ifstream& ifs); // 'z' in the name to distinguish from zlib.inflate
};
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