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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
*/
/*
* file: cmd.hpp
* created: Jan 17, 2018 Wed
*
* Interactive command-line session:
* - query records in Key-Value database
*/
#pragma once
#include <string>
// forward
struct Runopts;
enum CMD { EXIT, READ, INDEX };
class CmdSession
{
public:
CmdSession(){}
void run(Runopts & opts);
private:
void cmdRead(Runopts & opts, std::string & cmd);
void cmdIndex(Runopts & opts, std::string & cmd);
void cmdTest(Runopts & opts, std::string & cmd);
void cmd_max_ref_part(Runopts & opts, std::string & cmd); // ref idx=0 part=1
};
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