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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 <fstream>
#include <vector>
#include <atomic>
// forward
class Read;
struct Readstate;
class Readfeed;
struct Runopts;
class Izlib;
/*
* FASTX report's data and functionality common to both FASTX aligned and other (non-aligned) reports
*/
class ReportFxBase {
public:
ReportFxBase();
ReportFxBase(Runopts& opts);
void init(Runopts& opts);
/*
* init output file names. It has a different semantics than init(opts) above.
*/
void init(Readfeed& readfeed, Runopts& opts, std::vector<std::string>& fv, std::vector<std::fstream>& fsv, const std::string& fpfx, const std::string& pid_str);
void write_a_read(std::ostream& strm, Read& read, const int& dbg=0);
void write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last=false, const int& dbg = 0);
unsigned num_out; // number of aligned output files (1 | 2 | 4) depending on the output type below
/*
* output type: 255/2 -> ~120 possible types
* defines the number of the files to output
* out_type = mask | mask | mask ... where 'mask' depends on the specified option
*/
int out_type;
std::atomic<unsigned long> num_reads; // count of reads processed so far. Use For debugging.
std::atomic<unsigned long> num_hits; // count of hits
std::atomic<unsigned long> num_miss; // count of misses (other)
std::atomic<unsigned long> num_io_bad;
std::atomic<unsigned long> num_io_fail;
private:
/*
* 1-file 2-files paired paired_in paired_out out2 sout other
* x01 x02 x04 x08 x10 x20 x40 x80
*/
const int mask_1_file = 0x01;
const int mask_2_file = 0x02;
const int mask_paired = 0x04;
const int mask_paired_in = 0x08;
const int mask_paired_out = 0x10;
const int mask_out2 = 0x20;
const int mask_sout = 0x40;
const int mask_other = 0x80;
/*
* validate the output type
*/
void validate_out_type(Runopts& opts);
/*
* set number of output files: 1 | 2 | 4 - calculated depending on the selected options
*/
void set_num_out(Runopts& opts);
};
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