|
0
|
1
|
|
|
2 #ifndef __GLOBALS
|
|
|
3 #define __GLOBALS
|
|
|
4
|
|
|
5
|
|
|
6 #define MAX_STR 256
|
|
|
7 #define GC_BIN 1000
|
|
|
8
|
|
|
9 #define VERSION "0.34"
|
|
|
10 #define LAST_UPDATE "December 7, 2011"
|
|
|
11
|
|
|
12
|
|
|
13 enum MODETYPE {NONE, PREP, READSAM, CALL};
|
|
|
14
|
|
|
15 enum WINDOWTYPE {LW, SW, CW};
|
|
|
16
|
|
|
17 enum GENDERTYPE {AUTODETECT, MALE, FEMALE};
|
|
|
18
|
|
|
19 enum GENDERTYPE GENDER;
|
|
|
20
|
|
|
21 enum MODETYPE RUNMODE;
|
|
|
22
|
|
|
23 int num_chrom;
|
|
|
24 int MULTGC;
|
|
|
25 float MAX_GC_CORR;
|
|
|
26 float MIN_GC_CORR;
|
|
|
27 int VERBOSE;
|
|
|
28 int CHECKSAM;
|
|
|
29
|
|
|
30 static const int magicNum = 3111696;
|
|
|
31
|
|
|
32 char *GENOME_FASTA;
|
|
|
33 char *GENOME_GAPS;
|
|
|
34 char *GENOME_CONF;
|
|
|
35
|
|
|
36 int LW_SIZE;
|
|
|
37 int SW_SIZE;
|
|
|
38 int CW_SIZE;
|
|
|
39 int LW_SLIDE;
|
|
|
40 int SW_SLIDE;
|
|
|
41
|
|
|
42 float LW_MEAN;
|
|
|
43 float LW_STD;
|
|
|
44 float LW_MEAN_X;
|
|
|
45 float LW_STD_X;
|
|
|
46
|
|
|
47 float SW_MEAN;
|
|
|
48 float SW_STD;
|
|
|
49 float SW_MEAN_X;
|
|
|
50 float SW_STD_X;
|
|
|
51
|
|
|
52 float CW_MEAN;
|
|
|
53 float CW_STD;
|
|
|
54 float CW_MEAN_X;
|
|
|
55 float CW_STD_X;
|
|
|
56
|
|
|
57 int CONT_WINDOW;
|
|
|
58 int CUT_WINDOW;
|
|
|
59
|
|
|
60 typedef struct window{
|
|
|
61 int start;
|
|
|
62 int end;
|
|
|
63 float gc;
|
|
|
64 float depth;
|
|
|
65 char isControl;
|
|
|
66 }_window;
|
|
|
67
|
|
|
68 typedef struct chrom{
|
|
|
69 char *name;
|
|
|
70 int length;
|
|
|
71 int lw_cnt;
|
|
|
72 int sw_cnt;
|
|
|
73 int cw_cnt;
|
|
|
74 struct window *sw;
|
|
|
75 struct window *lw;
|
|
|
76 struct window *cw;
|
|
|
77 }_chrom;
|
|
|
78
|
|
|
79 struct chrom **chromosomes;
|
|
|
80
|
|
|
81 #endif
|
