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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
Mika�l Salson mikael.salson@lifl.fr
H�l�ne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/*
* @file output.hpp
* Created: Nov 06, 2017 Mon
* @brief Class for handling SMR output
*/
#pragma once
#include "report_fastx.h"
#include "report_fx_other.h"
#include "report_blast.h"
#include "report_denovo.h"
#include "report_sam.h"
#include "report_biom.h"
// forward
struct Index;
class References;
class Read;
class Refstats;
struct Readstats;
struct Runopts;
class KeyValueDatabase;
class Readfeed;
void writeReports(Readfeed& readfeed, Readstats& readstats, KeyValueDatabase& kvdb, Runopts& opts);
class Output {
public:
ReportFastx fastx; // fastx aligned report
ReportFxOther fx_other; // fastx non-aligned report
ReportBlast blast;
ReportDenovo denovo;
ReportSam sam;
ReportBiom biom;
Output(Readfeed& readfeed, Runopts& opts);
//~Output();
private:
void init(Readfeed& readfeed, Runopts& opts);
}; // ~class Output
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