1 /* $Id: oligo.h 214025 2018-03-05 07:06:43Z twu $ */ 2 #ifndef OLIGO_INCLUDED 3 #define OLIGO_INCLUDED 4 5 #include "bool.h" 6 #include "genomicpos.h" 7 #include "indexdb.h" 8 #include "reader.h" 9 10 typedef enum {INIT, DONE, INVALID, VALID} Oligostate_T; 11 12 extern Oligostate_T 13 Oligo_next_5 (Oligostate_T last_state, int *querypos, Oligospace_T *forward, 14 Oligospace_T *revcomp, Reader_T reader, int genestrand); 15 extern Oligostate_T 16 Oligo_next_3 (Oligostate_T last_state, int *querypos, Oligospace_T *forward, 17 Oligospace_T *revcomp, Reader_T reader, int genestrand); 18 19 extern Oligostate_T 20 Oligo_skip_5 (Oligostate_T last_state, int *querypos, Oligospace_T *forward, 21 Oligospace_T *revcomp, Reader_T reader, int genestrand, int nskip); 22 extern Oligostate_T 23 Oligo_skip_3 (Oligostate_T last_state, int *querypos, Oligospace_T *forward, 24 Oligospace_T *revcomp, Reader_T reader, int genestrand, int nskip); 25 26 extern void 27 Oligo_setup (int index1part, int mode); 28 29 #endif 30