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#ifndef BITREAD_H_
#define BITREAD_H_
/**
* WHAM - high-throughput sequence aligner
* Copyright (C) 2011 WHAM Group, University of Wisconsin
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
/* $Id: bitread.h 162 2012-07-31 09:14:04Z yinan $ */
#include "lib.h"
#define BITS_PER_BASE 3
#define BITS_PER_BASE_LL 3LL
#define BITS_PER_BYTE 8
#define BITS_PER_WORD 32
#define BITS_PER_LONGWORD 64
#define BITS_LONGWORD_SHIFT 6
#define BITS_LONGWORD_MASK 0x000000000000003f
#define BITS_TWO_LONGWORD 128
#define BITS_THREE_LONGWORD 192
#define BITS_FOUR_LONGWORD 256
#define BITS_FIVE_LONGWORD 320
#define WORDS_PER_READ 6
class BitRead {
public:
/*
* BitRead::extract
* extract a subsequence from the sequence. The subsequence
* starts from offset-th character of the sequence and has len
* characters.
*
* This implementation is highly optimized for modern CPUs. All IF
* statements are implemented by arithmetic operations to eliminate the
* branch. It support up to 256-bit sequence (85 bases) that can be
* fitted into four 64-bit integers.
*/
inline static void extract(int64 * a, int64 * b, int64 offset, int len) {
int shift = ((offset) + (len)) & BITS_LONGWORD_MASK;
int index = ((offset) + (len)) >> BITS_LONGWORD_SHIFT;
int64 mask = 0LL - (shift != 0);
int cshift = BITS_PER_LONGWORD - shift;
b[0] = (mask & (a[index - 5] >> cshift)) | (a[index - 6] << shift);
b[1] = (mask & (a[index - 4] >> cshift)) | (a[index - 5] << shift);
b[2] = (mask & (a[index - 3] >> cshift)) | (a[index - 4] << shift);
b[3] = (mask & (a[index - 2] >> cshift)) | (a[index - 3] << shift);
b[4] = (mask & (a[index - 1] >> cshift)) | (a[index - 2] << shift);
b[5] = (mask & (a[index] >> cshift)) | (a[index - 1] << shift);
shift = BITS_PER_LONGWORD - ((len) & BITS_LONGWORD_MASK);
b[0] = (0LL - (len > BITS_FIVE_LONGWORD)) & (b[0] << shift >> shift);
cshift = (0LL - (len < BITS_FIVE_LONGWORD)) & shift;
b[1] = b[1] << cshift >> cshift;
b[1] = (0LL - ((len) > BITS_FOUR_LONGWORD)) & b[1];
cshift = (0LL - (len < BITS_FOUR_LONGWORD)) & shift;
b[2] = b[2] << cshift >> cshift;
b[2] = (0LL - ((len) > BITS_THREE_LONGWORD)) & b[2];
cshift = (0LL - (len < BITS_THREE_LONGWORD)) & shift;
b[3] = b[3] << cshift >> cshift;
b[3] = (0LL - ((len) > BITS_TWO_LONGWORD)) & b[3];
cshift = (0LL - (len < BITS_TWO_LONGWORD)) & shift;
b[4] = b[4] << cshift >> cshift;
b[4] = (0LL - ((len) > BITS_PER_LONGWORD)) & b[4];
cshift = (0LL - (len < BITS_PER_LONGWORD)) & shift;
b[5] = b[5] << cshift >> cshift;
}
inline static void genHeadMask(int64 * mask, int l) {
int64 tmp[WORDS_PER_READ];
for (int i = 0; i < WORDS_PER_READ; i++)
tmp[i] = -1;
removeHead2(tmp, mask, l);
}
/*
* BitRead::removeHead
* This function is used to extract rightmost portion of sequence a
* into sequence b. The extracted portion has l bits.
*
* This implementation is highly optimized for modern CPUs. All IF
* statements are implemented by arithmetic operations to eliminate the
* branch. It support up to 256-bit sequence (85 bases) that can be
* fitted into four 64-bit integers.
*/
inline static void removeHead(int64 * a, int64 * b, int64 * mask) {
b[0] = a[0] & mask[0];
b[1] = a[1] & mask[1];
b[2] = a[2] & mask[2];
b[3] = a[3] & mask[3];
b[4] = a[4] & mask[4];
b[5] = a[5] & mask[5];
}
inline static void removeHead2(int64 * a, int64 * b, int l) {
int shift;
int lshift = BITS_PER_LONGWORD - ((l) & BITS_LONGWORD_MASK);
shift = lshift;
b[0] = ((int64) 0 - (l > BITS_FIVE_LONGWORD)) & (a[0] << shift >> shift);
shift = ((int64) 0 - (l < BITS_FIVE_LONGWORD)) & lshift;
b[1] = a[1] << shift >> shift;
shift = lshift;
b[1] = ((int64) 0 - ((l) > BITS_FOUR_LONGWORD)) & b[1];
shift = ((int64) 0 - (l < BITS_FOUR_LONGWORD)) & lshift;
b[2] = a[2] << shift >> shift;
shift = lshift;
b[2] = ((int64) 0 - ((l) > BITS_THREE_LONGWORD)) & b[2];
shift = ((int64) 0 - ((l) < BITS_THREE_LONGWORD)) & lshift;
b[3] = a[3] << shift >> shift;
shift = lshift;
b[3] = ((int64) 0 - ((l) > BITS_TWO_LONGWORD)) & b[3];
shift = ((int64) 0 - ((l) < BITS_TWO_LONGWORD)) & lshift;
b[4] = a[4] << shift >> shift;
shift = lshift;
b[4] = ((int64) 0 - ((l) > BITS_PER_LONGWORD)) & b[4];
shift = ((int64) 0 - ((l) < BITS_PER_LONGWORD)) & lshift;
b[5] = a[5] << shift >> shift;
}
/*
* BitRead::removeInterval
* This function is used to remove an interval segment from sequence a,
* and extract others into sequence b. The interval starts from x-th
* bit in the sequence and has len bits.
*
* This implementation is highly optimized for modern CPUs. All IF
* statements are implemented by arithmetic operations to eliminate the
* branch. It support up to 256-bit sequence (85 bases) that can be
* fitted into four 64-bit integers.
*
* This implementation requires that the sequence a is stored in the
* rightmost of seven 64-bit integers. All unoccupied bits in the seven
* 64-bit integers are set to be 0s.
*/
inline static void removeInterval(int64 * a, int64 * b, uint32 x, int p) {
int index1 = WORDS_PER_READ - 1 - ((x) >> BITS_LONGWORD_SHIFT);
int index2 = WORDS_PER_READ - 1 - (((x) + (p)) >> BITS_LONGWORD_SHIFT);
int shift = (x) & BITS_LONGWORD_MASK;
int shift2 = ((x) + (p)) & BITS_LONGWORD_MASK;
int poffset = (p) >> BITS_LONGWORD_SHIFT;
int pshift = (p) & BITS_LONGWORD_MASK;
int64 mask = ((int64) 0 - (shift != 0))
& ((int64) -1 >> (BITS_PER_LONGWORD - shift));
int64 mask2 = (int64) 0 - (pshift != 0);
int index3 = index1 - poffset;
int rpshift = BITS_PER_LONGWORD - pshift;
b[5] = a[5];
b[4] = a[4];
b[3] = a[3];
b[2] = a[2];
b[1] = a[1];
b[index1] = (a[index1] & mask) | (a[index2] >> shift2 << shift);
b[index1] |= ((int64) 0 - (shift2 > shift)) & ((a[index2 - 1] << rpshift));
b[index1 - 1] = (a[index3 - 1] >> pshift)
| (mask2 & (a[index3 - 2] << rpshift));
b[index1 - 2] = (a[index3 - 2] >> pshift)
| (mask2 & (a[index3 - 3] << rpshift));
b[index1 - 3] = (a[index3 - 3] >> pshift)
| (mask2 & (a[index3 - 4] << rpshift));
b[index1 - 4] = (a[index3 - 4] >> pshift)
| (mask2 & (a[index3 - 5] << rpshift));
b[index1 - 5] = (a[index3 - 5] >> pshift)
| (mask2 & (a[index3 - 6] << rpshift));
}
inline static void copy(int64 * a, int64 * b) {
b[5] = a[5];
b[4] = a[4];
b[3] = a[3];
b[2] = a[2];
b[1] = a[1];
b[0] = a[0];
}
inline static bool compare(int64 * a, int64 * b) {
return (a[0] == b[0]) && (a[1] == b[1]) && (a[2] == b[2]) && (a[3] == b[3])
&& (a[4] == b[4]) && (a[5] == b[5]);
}
inline static void leftShift(int64 * a, int64 * b) {
b[0] = (a[0] << 3) | (a[1] >> 61);
b[1] = (a[1] << 3) | (a[2] >> 61);
b[2] = (a[2] << 3) | (a[3] >> 61);
b[3] = (a[3] << 3) | (a[4] >> 61);
b[4] = (a[4] << 3) | (a[5] >> 61);
b[5] = (a[5] << 3);
}
inline static void rightShift(int64 * a, int64 * b) {
b[0] = (a[0] >> 3);
b[1] = (a[1] >> 3) | (a[0] << 61);
b[2] = (a[2] >> 3) | (a[1] << 61);
b[3] = (a[3] >> 3) | (a[2] << 61);
b[4] = (a[4] >> 3) | (a[3] << 61);
b[5] = (a[5] >> 3) | (a[4] << 61);
}
};
#endif /* BITREAD_H_ */
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