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