LIBRARY

#include <biolibc/vcf.h>
-lbiolibc -lxtend

SYNOPSIS

int bl_vcf_read_ss_call(bl_vcf_t *vcf_call, FILE *vcf_stream, vcf_field_mask_t field_mask)

ARGUMENTS

vcf_stream  FILE pointer to VCF input stream
vcf_call    bl_vcf_t structure to receive VCF data
field_mask  Bit mask to indicate which fields to store

DESCRIPTION

Read a single-sample VCF call (static fields and one sample column). This should only be used with VCF inputs that have exactly one sample column. For multisample VCFs, use bl_vcf_read_static_fields() followed by a loop to read the sample data.

If field_mask is not BL_VCF_FIELD_ALL, fields not indicated by a 1 in the bit mask are discarded rather than stored in bed_feature. Possible mask values are:

BL_VCF_FIELD_ALL BL_VCF_FIELD_CHROM BL_VCF_FIELD_POS BL_VCF_FIELD_ID BL_VCF_FIELD_REF BL_VCF_FIELD_ALT BL_VCF_FIELD_QUAL BL_VCF_FIELD_FILTER BL_VCF_FIELD_INFO BL_VCF_FIELD_FORMAT

RETURN VALUES

BL_READ_OK upon success BL_READ_TRUNCATED if EOF is encountered while reading a call BL_READ_EOF if EOF is encountered between calls as it should be

LIBRARY

SYNOPSIS

ARGUMENTS

DESCRIPTION

RETURN VALUES

SEE ALSO