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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
*/
#include "paralleltraversal.hpp"
#include <queue>
#ifndef minoccur_h
#define minoccur_h
/*
*
* FUNCTION : void find_minoccur ( int minlenread )
* PURPOSE : find the minimum possible occurrence of a k-mer in the database for which a parallel
* traversal of the universal Levenshtein automaton and the Burst trie is carried out
*
**************************************************************************************************************/
void find_minoccur ( int );
#ifdef WINDOWS
/*
*
* FUNCTION : int isnewline ( char *ch )
* PURPOSE : parse '\n', '\r' or '\r\n' newlines
* PARAMETERS : pointer to character being observed
*
**************************************************************************************************************/
int isnewline( char *ch );
#endif
/* rRNA database file (fasta) */
extern char *rrnadbfile;
/* the minimum number of occurrences of an s/2-mer hash id in the rrna database */
extern unsigned int MINOCCUR;
/* maximum/minimum length of an rRNA sequence in the database */
extern int maxlen;
extern int minlen;
/* the number of rRNAs in the rRNA database */
extern int rrnastrings;
extern unsigned int mask32;
extern char map_nt[122];
extern hashid *kmerf;
extern hashid *kmerr;
#endif
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