44 lines
1.6 KiB
C
44 lines
1.6 KiB
C
/*
|
|
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
|
|
*
|
|
* This file is part of HISAT 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.
|
|
*
|
|
* HISAT 2 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 HISAT 2. If not, see <http://www.gnu.org/licenses/>.
|
|
*/
|
|
|
|
#ifndef HIERGBWT_COMMON_H_
|
|
#define HIERGBWT_COMMON_H_
|
|
|
|
// maximum size of a sequence represented by a local index
|
|
static const uint32_t local_index_size = (1 << 16) - (1 << 13); // 1 << 5 is necessary for eftab index
|
|
static const uint32_t local_max_gbwt = (1 << 16) - (1 << 11);
|
|
|
|
// 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_fm = 6;
|
|
static const int32_t local_lineRate_gfm = 7;
|
|
|
|
// 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 /*HIERGBWT_COMMON_H_*/
|