81 lines
1.9 KiB
C++
81 lines
1.9 KiB
C++
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/*
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* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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*
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* This file is part of Bowtie 2.
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*
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* Bowtie 2 is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* Bowtie 2 is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include <stdint.h>
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/* Generated by gen_lookup_tables.pl */
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uint8_t cCntLUT_4[4][4][256];
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uint8_t cCntLUT_4_rev[4][4][256];
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uint8_t cCntBIT[8][256];
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int countCnt(int by, int c, uint8_t str) {
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int count = 0;
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if(by == 0) by = 4;
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while(by-- > 0) {
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int c2 = str & 3;
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str >>= 2;
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if(c == c2) count++;
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}
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return count;
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}
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int countCnt_rev(int by, int c, uint8_t str) {
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int count = 0;
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if(by == 0) by = 4;
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while(by-- > 0) {
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int c2 = (str >> 6) & 3;
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str <<= 2;
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if(c == c2) count++;
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}
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return count;
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}
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void initializeCntLut() {
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for(int by = 0; by < 4; by++) {
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for(int c = 0; c < 4; c++) {
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for(int str = 0; str < 256; str++) {
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cCntLUT_4[by][c][str] = countCnt(by, c, str);
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cCntLUT_4_rev[by][c][str] = countCnt_rev(by, c, str);
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}
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}
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}
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}
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int countBit(int b, uint8_t str) {
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int count = 0;
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if(b == 0) b = 8;
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while(b-- > 0) {
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if(str & 0x1) count++;
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str >>= 1;
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}
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return count;
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}
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void initializeCntBit() {
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for(int b = 0; b < 8; b++) {
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for(int str = 0; str < 256; str++) {
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cCntBIT[b][str] = countBit(b, str);
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}
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}
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}
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