izlib.hpp

/*
 @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 Noé      laurent.noe@lifl.fr
			   Pierre Pericard  pierre.pericard@lifl.fr
			   Daniel McDonald  wasade@gmail.com
			   Mikaël Salson    mikael.salson@lifl.fr
			   Hélène 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
};