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globals.h
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globals.h
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#ifndef __GLOBALS
#define __GLOBALS
#define MAX_STR 256
#define GC_BIN 1000
#define VERSION "1.3"
#define LAST_UPDATE "February 24, 2021"
enum MODETYPE {NONE, PREP, READSAM, CALL, CONC};
enum WINDOWTYPE {LW, SW, CW};
enum GENDERTYPE {AUTODETECT, MALE, FEMALE};
enum GENDERTYPE GENDER;
enum MODETYPE RUNMODE;
int ISNORMALIZED;
int num_chrom;
int num_pseudo;
int n_sam_b; // Begining sam file's index
int n_sam_e; // Terminating sam file's index
double memUsage;
int MULTGC;
float MAX_GC_CORR;
float MIN_GC_CORR;
int VERBOSE;
int CHECKSAM;
extern FILE *pseudo;
extern struct gapcell *pseudotable;
static const int magicNum = 74088;
static const int magicNumDepth = 1764;
char *GENOME_FASTA;
char *GENOME_GAPS;
char *GENOME_CONF;
char *GENOME_PSEUDO;
int LW_SIZE;
int SW_SIZE;
int CW_SIZE;
int LW_SLIDE;
int SW_SLIDE;
int PLOIDY;
float LW_MEAN;
float LW_STD;
float LW_MEAN_X;
float LW_STD_X;
float SW_MEAN;
float SW_STD;
float SW_MEAN_X;
float SW_STD_X;
float CW_MEAN;
float CW_STD;
float CW_MEAN_X;
float CW_STD_X;
int CONT_WINDOW;
int CUT_WINDOW;
int MIN_DUP;
typedef struct window{
int start;
int end;
float gc;
float depth;
char isControl;
}_window;
typedef struct chrom{
char *name;
int length;
int lw_cnt;
int sw_cnt;
int cw_cnt;
int dw_cnt;
struct window *sw;
struct window *lw;
struct window *cw;
struct window *dw;
}_chrom;
struct chrom **chromosomes;
#endif