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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 VERBOSE;
extern int PROFILE;
extern int SPACING;
extern double BEST_TIE;
extern char *SORT_PATH;
extern uint64 MEM_LIMIT;
extern uint64 MEM_PHYSICAL;
int Set_Filter_Params(int kmer, int suppress, int nthreads);
void *Sort_Kmers(DAZZ_DB *block, int *len);
void Match_Filter(DAZZ_DB *ablock, DAZZ_DB *bblock,
void *atable, int alen, void *btable, int blen, int comp, int start);
#define FLAG_DOA 0x1
#define FLAG_DOB 0x2
void Reporter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,
Align_Spec *asettings, int mflag);
void Clean_Exit(int val);
#endif
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