vcfutils.h

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/*
    Time will show if this module will be merged into others 
    or perhaps removed completely.
*/
#ifndef VCF_UTILS_H
#define VCF_UTILS_H

#include "vcf.h"


int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line);


void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask);


int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which);


#define GT_HOM_RR 0 // note: the actual value of GT_* matters, used in dosage r2 calculation
#define GT_HOM_AA 1
#define GT_HET_RA 2
#define GT_HET_AA 3
#define GT_HAPL_R 4
#define GT_HAPL_A 5
#define GT_UNKN   6
int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal);

static inline int bcf_acgt2int(char c)
{
    if ( (int)c>96 ) c -= 32;
    if ( c=='A' ) return 0;
    if ( c=='C' ) return 1;
    if ( c=='G' ) return 2;
    if ( c=='T' ) return 3;
    return -1;
}
#define bcf_int2acgt(i) "ACGT"[i]

#define bcf_ij2G(i, j) ((j)*((j)+1)/2+(i))

#endif