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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* 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/>.
*/
#ifndef BITARRAY_H
#define BITARRAY_H
/*
*
* bitArray.h
* declarations for bit arrays
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 07/14/2007 04:15:27 PM CEST
*
* SVN
* Revision of last commit: $Rev: 19 $
* Author: $Author: steve $
* Date: $Date: 2008-05-14 15:43:29 +0200 (Wed, 14 May 2008) $
*
* Id: $Id: bitArray.h 19 2008-05-14 13:43:29Z steve $
* Url: $URL: file:///homes/bierdepot/steve/svn/segemehl/trunk/libs/bitArray.h $
*/
typedef unsigned char* bitarray;
bitarray initbitarray(void *, Uint length);
void dumpbitarray(bitarray a, Uint len);
unsigned char valbitarray(bitarray a, Uint len, unsigned char val);
void setbitarray(bitarray a, Uint len, unsigned char val);
bitarray resizebitarray(void *space, bitarray, Uint len);
static inline void
setbit(bitarray a, Uint pos, unsigned char val) {
int bytes,
bits,
shift;
unsigned char byte, resc;
bytes = pos >> 3;
bits = pos & 7;
resc = a[bytes];
byte = (unsigned char) val;
shift = 7 ^ bits;
byte = byte << shift;
byte = byte ^ resc;
byte = byte & (1 << shift);
a[bytes] = byte ^ resc;
}
static inline unsigned char
getbit(bitarray a, Uint pos) {
int bytes,
bits;
unsigned char byte;
bytes = pos >> 3;
bits = pos & 7;
byte = a[bytes];
byte = byte >> (7 ^ bits);
byte = byte << 7;
byte = byte >> 7;
byte = byte & 1;
return byte;
}
#endif
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