1 /* $Id: diagnostic.h 40271 2011-05-28 02:29:18Z twu $ */
2 #ifndef DIAGNOSTIC_INCLUDED
3 #define DIAGNOSTIC_INCLUDED
4 
5 #define T Diagnostic_T
6 typedef struct T *T;
7 struct T {
8 #ifndef PMAP
9   double query_oligodepth;
10 #endif
11   int query_badoligos;
12   int query_repoligos;
13   int query_trimoligos;
14   int query_trim_start;
15   int query_trim_end;
16 
17   double stage1_runtime;
18   int firstpair_found_5;
19   int firstpair_found_3;
20   int stutter_searched_5;
21   int stutter_searched_3;
22   int stutter_nmatchpairs;
23   int stutter_matches_5;
24   int stutter_matches_3;
25   int dangling_5;
26   int dangling_3;
27   int dangling_nmatchpairs;
28 
29   int sampling_rounds;
30   int sampling_nskip;
31   int ngregions;
32 };
33 
34 extern void
35 Diagnostic_free (T *old);
36 
37 extern T
38 Diagnostic_new ();
39 
40 extern void
41 Diagnostic_print (T this);
42 
43 
44 #undef T
45 #endif
46 
47