/*
* Copyright 2013, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of Beast. Beast is based on Bowtie 2.
*
* Beast is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beast 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Beast. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef HIEREBWT_COMMON_H_
#define HIEREBWT_COMMON_H_
// maximum size of a sequence represented by a local index
static const uint32_t local_index_size = (1 << 16) - (1 << 8); // 1 << 5 is necessary for eftab index
// size of the overlapped sequence between the sequences represented by two consecutive local indexes
static const uint32_t local_index_overlap = 1024;
// interval between two consecutive local indexes
static const uint32_t local_index_interval = local_index_size - local_index_overlap;
// line rate in local indexes
static const int32_t local_lineRate = 6;
// how many rows are marked in a local index, every 2^<int>th row is marked
static const int32_t local_offRate = 3;
// the look table in a local index 4^<int> entries
static const int32_t local_ftabChars = 6;
#endif /*HIEREBWT_COMMON_H_*/