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/******************************************************************************
* Copyright © 2009-2016 -- LIRMM/CNRS *
* (Laboratoire d'Informatique, de Robotique et de *
* Microélectronique de Montpellier / *
* Centre National de la Recherche Scientifique) *
* LIFL/INRIA *
* (Laboratoire d'Informatique Fondamentale de *
* Lille / Institut National de Recherche en *
* Informatique et Automatique) *
* LITIS *
* (Laboratoire d'Informatique, du Traitement de *
* l'Information et des Systèmes). *
* *
* Copyright © 2011-2016 -- IRB/INSERM *
* (Institut de Recherches en Biothérapie / *
* Institut National de la Santé et de la Recherche *
* Médicale). *
* *
* Copyright © 2015-2016 -- AxLR/SATT *
* (Lanquedoc Roussilon / *
* Societe d'Acceleration de Transfert de *
* Technologie). *
* *
* Programmeurs/Progammers: *
* Nicolas PHILIPPE <nphilippe.resear@gmail.com> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Jérôme Audoux <jerome.audoux@gmail.com> *
* with additional contribution for the packaging of: *
* Alban MANCHERON <alban.mancheron@lirmm.fr> *
* *
* Contact: CRAC list <crac-bugs@lists.gforge.inria.fr> *
* Paper: CRAC: An integrated RNA-Seq read analysis *
* Philippe N., Salson M., Commes T., Rivals E. *
* Genome Biology 2013; 14:R30. *
* *
* ------------------------------------------------------------------------- *
* *
* This File is part of the CRAC program. *
* *
* 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 BASICSINCLUDED
#define BASICSINCLUDED
#include <sys/types.h>
#include <sys/resource.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define mask31 0x0000001F
#define max(x,y) ((x)>(y)?(x):(y))
#define min(x,y) ((x)<(y)?(x):(y))
/*numero de bits del entero de la maquina*/
#define W 32
/* W-1 */
#define Wminusone 31
/*numero de bits del entero de la maquina*/
#define WW 64
/*bits para hacer la mascara para contar mas rapido*/
#define bitsM 8
/*bytes que hacen una palabra */
#define BW 4
#define size_uchar 256
/* bits needed to represent a number between 0 and n */
inline uint bits (uint n){
uint b = 0;
while (n) { b++; n >>= 1; }
return b;
}
/* reads bit p from e */
#define bitget(e,p) ((((e)[(p)/W] >> ((p)%W))) & 1)
/* sets bit p in e */
#define bitset(e,p) ((e)[(p)/W] |= (1<<((p)%W)))
/* cleans bit p in e */
#define bitclean(e,p) ((e)[(p)/W] &= ~(1<<((p)%W)))
/* numero de enteros necesarios para representar e elementos de largo n */
#define enteros(e,n) ((e)*(n))/W+(((e)*(n))%W > 0)
inline ulong GetField(ulong *A, register ulong len, register ulong index) {
register ulong i=index*len/W, j=index*len-W*i, result;
if (j+len <= W)
result = (A[i] << (W-j-len)) >> (W-len);
else {
result = A[i] >> j;
result = result | (A[i+1] << (WW-j-len)) >> (W-len);
}
return result;
}
inline void SetField(ulong *A,register ulong len, register ulong index,register ulong x) {
ulong i=index*len/W, j=index*len-i*W;
ulong mask = ((j+len) < W ? ~0u << (j+len) : 0) | ((W-j) < W ? ~0u >> (W-j) : 0);
A[i] = (A[i] & mask) | x << j;
if (j+len>W) {
mask = ((~0u) << (len+j-W));
A[i+1] = (A[i+1] & mask)| x >> (W-j);
}
}
inline unsigned GetFieldW32(unsigned *A,register unsigned index) {
return A[index];
}
inline void SetField32(unsigned *A, register unsigned index,register unsigned x) {
A[index]=x;
}
inline unsigned GetFieldW16(unsigned *A,register unsigned index) {
register unsigned i=index/2, j=(index&1)<<4, result;
result = (A[i] << (16-j)) >> (16);
return result;
}
inline unsigned GetFieldW4(unsigned *A,register unsigned index) {
register unsigned i=index/8, j=(index&0x7)<<2;
/*register unsigned i=index/8, j=index*4-32*i; */
return (A[i] << (28-j)) >> (28);
}
#endif
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