filter.h

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*   Eugene W. Myers Jr.                                                              *
*   Bautzner Str. 122e                                                               *
*   01099 Dresden                                                                    *
*   GERMANY                                                                          *
*   Email: gene.myers@gmail.com                                                      *
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/*******************************************************************************************
 *
 *  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 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