rafreader.h

#ifndef RAFREADER_INCLUDED
#define RAFREADER_INCLUDED
 
#include "typedefs.h"
#include <stdio.h>
 
#define RAFSTRSIZE 20
 
typedef uint64_t bits_t;
 
struct RAFReader {
    char       *fname;
    FILE       *fp;
    Tokenizer  *tkz;
    int         ispipe;         // 1 if fp is a pipe; 0 otherwise
 
    // properties of current snp
    long        snpid;          // 0-based index of current snp
    char ref[RAFSTRSIZE];       // reference allele
    char alt[RAFSTRSIZE];       // alternate alleles
    char chr[RAFSTRSIZE];       // chromosome
    unsigned long nucpos;       // nucleotide position from raf file
    double      raf;            // frequency of reference allele
    double      daf;            // frequency of derived allele
};
 
RAFReader  *RAFReader_new(const char *fname);
void        RAFReader_clearChromosomes(int n, RAFReader *r[n]);
void        RAFReader_free(RAFReader * self);
int         RAFReader_next(RAFReader * self);
double      RAFReader_raf(RAFReader * r);
double      RAFReader_daf(RAFReader * r);
int         RAFReader_alleleCheck(int n, RAFReader * r[n]);
void        RAFReader_printHdr(FILE *fp);
void        RAFReader_print(RAFReader *r, FILE *fp);
void        RAFReader_printArray(int n, RAFReader * r[n], FILE *fp);
int         RAFReader_rewind(RAFReader *self);
int         RAFReader_multiNext(int n, RAFReader * r[n]);
int         RAFReader_findDaf(int n, RAFReader * r[n]);
static inline const char *RAFReader_chr(RAFReader *self);
static inline unsigned long RAFReader_nucpos(RAFReader *self);
static inline const char *RAFReader_ref(RAFReader *self);
static inline const char *RAFReader_alt(RAFReader *self);
static inline const char *RAFReader_fname(RAFReader *self);
 
static inline const char *RAFReader_fname(RAFReader *self) {
    return self->fname;
}    
 
static inline const char *RAFReader_chr(RAFReader *self) {
    return self->chr;
}
 
static inline const char *RAFReader_ref(RAFReader *self) {
    return self->ref;
}
 
static inline const char *RAFReader_alt(RAFReader *self) {
    return self->alt;
}
 
static inline unsigned long RAFReader_nucpos(RAFReader *self) {
    return self->nucpos;
}
#endif