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