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report_fastx.h
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report_fastx.h
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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 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
*/
#pragma once
#include "report.h"
#include "report_fx_base.h"
// forward
class Read;
class ReportFastx: public Report
{
public:
ReportFastx(Runopts& opts);
ReportFastx(Readfeed& readfeed, Runopts& opts);
void init(Readfeed& readfeed, Runopts& opts) override;
/*
* called on each read or each pair of reads (if paired)
* writes to aliged.fasta
*
* @param id processing thread enumerator 0,1,2..
* @param reads: 1 or 2 (paired) reads
* @param opts
* @param is_last flags the passed read is the last
*/
void append(const uint32_t& id, std::vector<Read>& reads, const Runopts& opts, const bool& is_last=false);
ReportFxBase& getBase();
private:
ReportFxBase base;
};