filter.h

/************************************************************************************\
*                                                                                    *
* Copyright (c) 2014, Dr. Eugene W. Myers (EWM). All rights reserved.                *
*                                                                                    *
* Redistribution and use in source and binary forms, with or without modification,   *
* are permitted provided that the following conditions are met:                      *
*                                                                                    *
*  · Redistributions of source code must retain the above copyright notice, this     *
*    list of conditions and the following disclaimer.                                *
*                                                                                    *
*  · Redistributions in binary form must reproduce the above copyright notice, this  *
*    list of conditions and the following disclaimer in the documentation and/or     *
*    other materials provided with the distribution.                                 *
*                                                                                    *
*  · The name of EWM may not be used to endorse or promote products derived from     *
*    this software without specific prior written permission.                        *
*                                                                                    *
* THIS SOFTWARE IS PROVIDED BY EWM ”AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES,    *
* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND       *
* FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL EWM BE LIABLE   *
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES *
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS  *
* OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY      *
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING     *
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN  *
* IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.                                      *
*                                                                                    *
* For any issues regarding this software and its use, contact EWM at:                *
*                                                                                    *
*   Eugene W. Myers Jr.                                                              *
*   Bautzner Str. 122e                                                               *
*   01099 Dresden                                                                    *
*   GERMANY                                                                          *
*   Email: gene.myers@gmail.com                                                      *
*                                                                                    *
\************************************************************************************/

/*******************************************************************************************
 *
 *  Filter interface for the dazzler.
 *
 *  Author:  Gene Myers
 *  Date  :  July 2013
 *
 ********************************************************************************************/

#ifndef _FILTER

#define _FILTER

#include "DB.h"
#include "align.h"

extern int    BIASED;
extern int    VERBOSE;
extern int    MINOVER;
extern int    HGAP_MIN;
extern int    SYMMETRIC;
extern int    IDENTITY;

extern uint64 MEM_LIMIT;
extern uint64 MEM_PHYSICAL;

#define NTHREADS  4    //  Must be a power of 2
#define NSHIFT    2    //  log_2 NTHREADS

int Set_Filter_Params(int kmer, int binshift, int suppress, int hitmin); 

void Build_Table(HITS_DB *block);

void Match_Filter(char *aname, HITS_DB *ablock, char *bname, HITS_DB *bblock,
                  int self, int comp, Align_Spec *asettings);

#endif