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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
*/
/*
* @file kseq_load.hpp
* @brief Function and variable definitions for kseq_load.cpp
*/
#ifndef KSEQ_LOAD_H
#define KSEQ_LOAD_H
#include "common.hpp"
#include "kseq.h"
#ifdef HAVE_LIBZ
#include <zlib.h>
KSEQ_INIT(gzFile, gzread)
#else
KSEQ_INIT(int, read)
#endif
/*! @fn load_reads()
@brief load reads into buffer using kseq library
@param char* inputreads
@param char* raw
@param uint64_t number_total_read
@param off_t full_file_size
@param char*& finalnt
@return char** reads
@version Feb 08, 2016
*/
char**
load_reads(char* inputreads,
char*& raw,
uint64_t number_total_read,
off_t full_file_size,
char*& finalnt);
#endif
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