vcfutils.c File Reference

#include "htslib/vcfutils.h"

Macros
#define	BRANCH_INT(type_t)
#define	BRANCH_INT(type_t, vector_end)
#define	BRANCH_INT(type_t, vector_end)
#define	BRANCH(type_t, vector_end)
#define	BRANCH(type_t, is_vector_end)
#define	BRANCH(type_t, is_vector_end)
#define	BRANCH(type_t, is_vector_end)
#define	BRANCH(type_t, is_vector_end)

Functions
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)
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 rm_mask)

Macro Definition Documentation

#define BRANCH	(		type_t,
			vector_end
	)

Value:

{ \
        for (i=0; i<line->n_sample; i++) \
        { \
            type_t *p = (type_t*) (gt->p + i*gt->size); \
            int ial; \
            for (ial=0; ial<gt->n; ial++) \
            { \
                if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
                if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
                if ( (p[ial]>>1)-1 >= line->n_allele ) return -1; \
                ac[(p[ial]>>1)-1]++; \
            } \
        } \
    }

#define BRANCH	(		type_t,
			is_vector_end
	)

Value:

{ \
                type_t *ptr = (type_t*) dat; \
                int size = sizeof(type_t); \
                for (j=0; j<ntop; j++) /* j:ori, k:new */ \
                { \
                    if ( is_vector_end ) { memcpy(dat+k*size, dat+j*size, size); break; } \
                    if ( rm_mask & 1<<(j+inc) ) continue; \
                    if ( j!=k ) memcpy(dat+k*size, dat+j*size, size); \
                    k++; \
                } \
            }

#define BRANCH	(		type_t,
			is_vector_end
	)

Value:

{ \
                type_t *ptr = (type_t*) dat; \
                int size = sizeof(type_t); \
                for (j=0; j<nR_ori; j++) \
                { \
                    for (k=0; k<=j; k++) \
                    { \
                        l_ori++; \
                        if ( is_vector_end ) { memcpy(dat+l_new*size, dat+l_ori*size, size); break; } \
                        if ( rm_mask & 1<<j || rm_mask & 1<<k ) continue; \
                        if ( l_ori!=l_new ) memcpy(dat+l_new*size, dat+l_ori*size, size); \
                        l_new++; \
                    } \
                } \
            }

#define BRANCH	(		type_t,
			is_vector_end
	)

Value:

{ \
                for (j=0; j<line->n_sample; j++) \
                { \
                    type_t *ptr_src = ((type_t*)dat) + j*nori; \
                    type_t *ptr_dst = ((type_t*)dat) + j*nA_new; \
                    int size = sizeof(type_t); \
                    int k_src, k_dst = 0; \
                    for (k_src=0; k_src<ntop; k_src++) \
                    { \
                        if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); break; } \
                        if ( rm_mask & 1<<(k_src+inc) ) continue; \
                        if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
                        k_dst++; \
                    } \
                } \
            }

#define BRANCH	(		type_t,
			is_vector_end
	)

#define BRANCH_INT

(

type_t

)

Value:

{        \
                type_t *p = (type_t *) ac_ptr;  \
                for (i=0; i<ac_len; i++)        \
                {                               \
                    ac[i+1] = p[i];             \
                    nac += p[i];                \
                }                               \
            }

#define BRANCH_INT	(		type_t,
			vector_end
	)

Value:

{ \
            for (i=0; i<line->n_sample; i++) \
            { \
                type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
                int ial; \
                for (ial=0; ial<fmt_gt->n; ial++) \
                { \
                    if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
                    if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
                    ac[(p[ial]>>1)-1]++; \
                } \
            } \
        }

#define BRANCH_INT	(		type_t,
			vector_end
	)

Value:

{ \
        type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \
        for (i=0; i<fmt_ptr->n; i++) \
        { \
            if ( p[i] == vector_end ) break; /* smaller ploidy */ \
            if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \
            int tmp = p[i]>>1; \
            if ( tmp>1 ) \
            { \
                if ( !ial ) { ial = tmp; has_alt = 1; } \
                else if ( tmp!=ial ) \
                { \
                    if ( tmp<ial ) \
                    { \
                        jal = ial; \
                        ial = tmp; \
                    } \
                    else \
                    { \
                        jal = tmp; \
                    } \
                    has_alt = 2; \
                } \
            } \
            else has_ref = 1; \
            nals++; \
        } \
    }

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