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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
*/
#pragma once
#include <vector>
#include <fstream>
#include "readstate.h"
#include "readfile.h"
#include "izlib.hpp"
// forward
class Readfeed;
struct Runopts;
/*
* base class for writing reports
*/
class Report
{
public:
Report(Runopts& opts);
virtual ~Report() = 0;
virtual void init(Readfeed& readfeed, Runopts& opts) = 0;
/*
* merge split report files.
* override if necessary
*/
virtual void merge(const uint32_t& num_splits, const uint32_t& num_out, const int& dbg = 0);
/*
* init zip interface. So far common to all the reports.
*/
virtual void init_zip();
void openfr(unsigned idx); // open a single file for reading
/*
* open report files for writing
* @param dbg debug level, see 'Runopts.dbg_level'
*/
void openfw(const int& dbg=0);
/*
* open selected report file for writing
* @param idx index into the array of report files
* @param dbg debug level as in 'Runopts.dbg_level'
*/
void openfw(const uint32_t& idx, const int& dbg=0); // close selected report file
void closef(const int& dbg=0); // close report files
void closef(const uint32_t& idx, const int& dbg=0); // close a file
int finish_deflate();
/*
* strip the split suffix from the output file name
* and rename the final output e.g.
* 'aligned_0.blast -> aligned.blast'
* @param path e.g. $HOME/sortmerna/run/out/aligned_0.blast
* @param sfx e.g. '_0'
*/
void strip_path_sfx(std::string& path, std::string sfx="_0");
protected:
std::string pid_str; // std::to_string(getpid());
bool is_zip; // flags the report is compressed
std::vector<std::string> fv; // report files
std::vector<std::fstream> fsv;
// reading compressed out files when merging the final output
std::vector<Izlib> vzlib_in;
std::vector<Readstate> vstate_in;
// writing compressed output during report generation and the final compressed output
std::vector<Izlib> vzlib_out;
std::vector<Readstate> vstate_out;
};
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