1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
|
/*******************************************************************************************
*
* Filter interface for the dazzler.
*
* Author: Gene Myers
* Date : July 2013
*
********************************************************************************************/
#ifndef _FILTER
#define _FILTER
#include "DB.h"
#include "align.h"
#undef PROFILE
extern int VERBOSE; // -v flag is set?
extern int MINOVER; // minimum overlap (-l)
extern int HGAP_MIN; // HGap minimum (-H)
extern int SYMMETRIC; // output both A vs B and B vs A? ( ! -A)
extern int IDENTITY; // compare reads against themselves? (-I)
extern int BRIDGE; // bridge consecutive, chainable alignments (-B)
extern char *SORT_PATH; // where to place temporary files (-P)
extern uint64 MEM_LIMIT; // memory limit (-M)
extern uint64 MEM_PHYSICAL;
void Set_Filter_Params(int kmer, int mod, int binshift, int suppress, int hitmin, int nthreads);
void *Sort_Kmers(DAZZ_DB *block, int *len);
void Match_Filter(char *aname, DAZZ_DB *ablock, char *bname, DAZZ_DB *bblock,
void *atable, int alen, void *btable, int blen, Align_Spec *asettings);
void Clean_Exit(int val);
#endif
|
