vcfutils.h

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/*  vcfutils.h -- allele-related utility functions.

    Copyright (C) 2012, 2013 Genome Research Ltd.

    Author: Petr Danecek <pd3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#ifndef HTSLIB_VCFUTILS_H
#define HTSLIB_VCFUTILS_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