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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 bitvector.hpp
* @brief Function and variable definitions for bitvector.cpp
*/
/** @file bitvector.hpp */
#ifndef BITVECTOR_H
#define BITVECTOR_H
/* for map matrix */
#include "indexdb.hpp"
/* a bitvector of 1 byte */
#define UCHAR unsigned char
/* mask for depth > 0 bitvectors for k = 1 */
#define MSB4 (UCHAR)4
/* mask for depth = 0 bitvectors for k = 1 */
#define MSB8 (UCHAR)8
/* initialized in paralleltraversal.cpp */
extern int _win_num;
extern int thiswindow;
extern int _readn;
extern int thisread;
/*
*
* FUNCTION : void init_win_k1 ( char*, MYBITSET*, MYBITSET* )
* PURPOSE : create the first bitvector table of the 17-mer window on the read at position i = 0.
* PARAMETERS :
*
**************************************************************************************************************/
void init_win_f ( char*, UCHAR*, UCHAR*, int numbvs );
void init_win_r ( char*, UCHAR*, UCHAR*, int numbvs );
/*
*
* FUNCTION : void offset_win_k1 ( char*, char*, MYBITSET*, MYBITSET*, MYBITSET* )
* PURPOSE : for each 17-mer window after the first one on the read, the bitvector table is
* computed from the previous one by means of bitshifting and looking only at the new character
* of the read
* PARAMETERS :
*
*
**************************************************************************************************************/
void offset_win_k1 ( char*, char*, UCHAR*, UCHAR*, UCHAR*, int numbvs );
/*
*
* FUNCTION : void output_win_k1 ( MYBITSET*, bool )
* PURPOSE : output the bitvector table (for debugging)
* PARAMETERS :
*
**************************************************************************************************************/
void output_win_k1 (UCHAR*, bool, int partialwin );
#endif
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