bl_vcf_rea...atic_fields(3) Library Functions Manual bl_vcf_rea...atic_fields(3) NAME bl_vcf_read_static_fields() - Read static VCF fields LIBRARY #include <biolibc/vcf.h> -lbiolibc -lxtend SYNOPSIS int bl_vcf_read_static_fields(bl_vcf_t *vcf_call, FILE *vcf_stream, vcf_field_mask_t field_mask) ARGUMENTS vcf_stream FILE stream for VCF input vcf_call Pointer to bl_vcf_t structure to receive fields field_mask Bit mask indicating which fields should be stored DESCRIPTION Read static fields (columns 1 to 9) from one line of a VCF file. This function does not read any of the sample data in columns 10 and on. Sam- ples can be read using a loop with tsv_read_field(3). 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 read- ing a call BL_READ_EOF if EOF is encountered between calls as it should be EXAMPLES FILE *stream; bl_vcf_t vcf_call; char sample_data[MAX_CHARS + 1]; size_t len; bl_vcf_read_static_fields(stream, &vcf_call, BL_VCF_FIELD_ALL); while ( tsv_read_field(stream, sample_data, MAX_CHARS, &len) != 'n' ) { ... } SEE ALSO bl_vcf_write_static_fields(3), bl_vcf_read_ss_call(3), bl_vcf_write_ss_call(3) bl_vcf_rea...atic_fields(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | EXAMPLES | SEE ALSO
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