vcfutils.h File Reference

#include "vcf.h"

Go to the source code of this file.

Macros
#define	GT_HOM_RR   0
#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
#define	bcf_int2acgt(i)   "ACGT"[i]
#define	bcf_ij2G(i, j)   ((j)*((j)+1)/2+(i))

Functions
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)
int	bcf_gt_type (bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal)

Macro Definition Documentation

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

bcf_ij2G() - common task: allele indexes to Number=G index (diploid) ,j: allele indexes, 0-based, i<=j

Returns index to the Number=G diploid array

#define bcf_int2acgt

(

i

)

"ACGT"[i]

#define GT_HAPL_A   5

#define GT_HAPL_R   4

#define GT_HET_AA   3

#define GT_HET_RA   2

#define GT_HOM_AA   1

#define GT_HOM_RR   0

bcf_gt_type() - determines type of the genotype : the GT format field as set for example by set_fmt_ptr : sample index (starting from 0) : index of the 1st non-reference allele (starting from 1) : index of the 2nd non-reference allele (starting from 1)

Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA, GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial is not NULL and the genotype has one or more non-reference alleles, $ial will be set. In case of GT_HET_AA, $ial is the position of the allele which appeared first in ALT. If $jal is not null and the genotype is GT_HET_AA, $jal will be set and is the position of the second allele in ALT.

#define GT_UNKN   6

Function Documentation

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

bcf_calc_ac() - calculate the number of REF and ALT alleles : for access to BCF_DT_ID dictionary VCF line obtained from vcf_parse1 : array of length line->n_allele : determine if INFO/AN,AC and indv fields be used

Returns 1 if the call succeeded, or 0 if the value could not be determined.

The value of determines if existing INFO/AC,AN can be used (BCF_UN_INFO) and and if indv fields can be splitted (BCF_UN_FMT).

int bcf_gt_type	(	bcf_fmt_t *	fmt_ptr,
		int	isample,
		int *	ial,
		int *	jal
	)

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

bcf_remove_alleles() - remove ALT alleles according to bitmask : for access to BCF_DT_ID dictionary VCF line obtained from vcf_parse1 : alleles to remove

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

bcf_trim_alleles() - remove ALT alleles unused in genotype fields : for access to BCF_DT_ID dictionary VCF line obtain from vcf_parse1

Returns the number of removed alleles on success or negative on error: -1 .. some allele index is out of bounds