interc_sv.h

#ifndef INTER_C_SV
#define INTER_C_SV
#include "vector.h"
#include "readbam.h"
#include "interval10X.h"
#include "common.h"
#include "valorconfig.h"

typedef struct inter_interval_pair{
	int start1;
	int start2;
	int end1;
	int end2;
	int chr1;
	int chr2;	
    unsigned long barcode;
} inter_interval_pair;
typedef inter_interval_pair inter_split_molecule_t;

typedef struct inter_sv_call{
    inter_interval_pair break_points;
    int supports[3];
    int cluster_size;
    sv_type type;
}inter_sv_call_t;
// inter-chrosomal svs
typedef struct ic_sv{
	inter_split_molecule_t AB;
	inter_split_molecule_t CD;
	interval_pair EF;
	int chr_source :16;
	int chr_target :16;
	sv_type type;
	unsigned char supports[3];

    short tabu;
	int dv :30;
	int covered :1;
	int inactive :1;
}ic_sv_t;



#define INTERC_BACK_COPY 4
#define INTERC_FORW_COPY 2


void ic_sv_bed_print(FILE *stream, ic_sv_t *sv);
void inter_sv_call_bed_print(FILE *stream, inter_sv_call_t *sv);


int interc_sv_comp(const void *, const void *);
int interc_sv_compd(const void *, const void *, size_t);
size_t barcode_binary_search(vector_t *mols, unsigned long key);

int inter_split_overlaps(inter_split_molecule_t s1, inter_split_molecule_t s2, int relax);

inter_split_molecule_t *inter_split_init(barcoded_read_pair *pair, interval_10X *a, interval_10X *b);

int inter_split_indicates_translocation(inter_split_molecule_t s1, inter_split_molecule_t s2, sv_type type);

ic_sv_t *inter_sv_init(inter_split_molecule_t *s1, inter_split_molecule_t *s2, interval_pair *tra_del ,sv_type type);

size_t split_molecule_binary_search(vector_t *splits, interval_10X key);
void filter_unsupported_pm_splits(vector_t *splits, vector_t *discordants);
vector_t *find_direct_translocations(vector_t *sp1, vector_t *sp2, vector_t **molecules);
int is_inter_chr_split(barcoded_read_pair *pair, interval_10X *a, interval_10X *b);


// returns a vector of inter_split_molecules
vector_t *find_separated_molecules(vector_t *reads, vector_t *mol_a, vector_t *mol_b);



vector_t *find_interchromosomal_events_lowmem(vector_t **molecules, bam_vector_pack **intra, char *bamname);
//vector_t *find_interchromosomal_events(vector_t **molecules, bam_vector_pack **reads);
#endif