1 /* $Id: comp.h 195548 2016-08-02 17:18:50Z twu $ */ 2 #ifndef COMP_INCLUDED 3 #define COMP_INCLUDED 4 5 /* Non-gap */ 6 #define MATCH_COMP '|' 7 #define DYNPROG_MATCH_COMP '*' 8 #define AMBIGUOUS_COMP ':' 9 #define MISMATCH_COMP ' ' 10 #define INDEL_COMP '-' 11 #define SHORTGAP_COMP '~' /* Prints as INDEL_COMP, but scores as NONINTRON_COMP */ 12 #define DIAGNOSTIC_SHORTEXON_COMP 's'/* Used only at print time */ 13 14 /* Gap */ 15 #define FWD_CANONICAL_INTRON_COMP '>' 16 #define FWD_GCAG_INTRON_COMP ')' 17 #define FWD_ATAC_INTRON_COMP ']' 18 #define REV_CANONICAL_INTRON_COMP '<' 19 #define REV_GCAG_INTRON_COMP '(' 20 #define REV_ATAC_INTRON_COMP '[' 21 22 #define NONINTRON_COMP '=' 23 #define DUALBREAK_COMP '#' 24 #define EXTRAEXON_COMP '^' 25 26 #define INTRONGAP_COMP '.' 27 #define INTRONGAP_CHAR '.' 28 29 30 #ifdef PMAP 31 #define BACKTRANSLATE_CHAR '?' 32 #endif 33 34 35 36 #endif 37