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drompa_gv.h
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/* Copyright(c) Ryuichiro Nakato <[email protected]>
* This file is a part of DROMPA sources.
*/
#ifndef _DROMPA_GV_H_
#define _DROMPA_GV_H_
#include <stdbool.h>
#include "common.h"
#include "seq.h"
#define BINSIZE_DEFAULT 100
#define BINSIZE_BROAD 1000
#define BINSIZE_DEFAULT_GV 100000
#define SMOOTHING_DEFAULT 500
#define SMOOTHING_BROAD 10000
#define WIDTH4LAMBDA_DEFAULT 100000
#define PEAKNUM_DEFAULT 10000
#define GCSIZE_DEFAULT 500000
#define GDSIZE_DEFAULT 500000
#define ENRICHTHRE_DEFAULT 2
#define PTHRE_INTERNAL_DEFAULT 1e-4
#define PTHRE_ENRICH_DEFAULT 1e-4
#define QTHRE_DEFAULT 1e-3
typedef enum{
FTYPE_PEAKCALL_SHARP,
FTYPE_PEAKCALL_BROAD,
FTYPE_PEAKCALL_E,
FTYPE_GV,
FTYPE_PD,
FTYPE_FRIP,
FTYPE_COMPARE_INTENSITY,
FTYPE_MULTICI,
FTYPE_COMPARE_GENEBODY,
FTYPE_GOVERLOOK,
FTYPE_PROFILE,
FTYPE_HEATMAP,
FTYPE_TR
} Function_Type;
typedef enum{
OWTYPE_NONE,
OWTYPE_RATIO,
OWTYPE_P_INTER,
OWTYPE_P_ENRICH,
} OUTPUTWIG_Type;
typedef enum{
TYPE_RATIO_NONE,
TYPE_RATIO_TOTALREAD,
TYPE_RATIO_NCIS,
CHIPNORMALIZETYPENUM
} ChIPNormalize_Type;
typedef struct{
int samplenum, samplenum_1st, samplenum_overlay;
char *headname;
int smoothing;
int width4lambda;
int flen;
Function_Type ftype;
PWfile_Type itype;
ChIPNormalize_Type ntype;
char *gtfile;
char *mpfile;
double mpthre;
char *gapfile;
bool includeYM;
int outputwig;
PWfile_Type wtype;
int showzero;
char *output_dir;
double IPmaxthre;
double enrichthre;
double pthre_internal, pthre_enrich;
double qthre;
/*ignore region*/
BedFile **igregion;
int n_igregion;
} DrParam;
typedef struct{
double ratio;
} LCstats;
typedef struct _LibCompare{
LCstats *genome, *chr;
} LibCompare;
typedef struct{
long nread;
} Library;
typedef struct _Samplefile{
char *argv;
Library *genome, *chr;
TYPE_WIGARRAY *data;
double lambda;
double nb_p, nb_n, nb_p0;
} Samplefile;
typedef struct{
double *IP;
double *Input;
double **SE, *SEarray;
double IPsum, Inputsum;
} Profile;
typedef struct{
Samplefile *ChIP, *Input;
LibCompare *comp;
int copyC, copyI, copycomp;
int overlay;
Peak *peak;
char *peak_argv;
char *peakarray;
char *linename;
int binsize;
int *binnum;
double scale_tag;
double scale_ratio;
double scale_pvalue;
Profile profile;
} SamplePair;
extern char str_ftype[][17];
#endif /* _DROMPA_GV_H_ */