NAME

bl_vcf_get_sample_ids() - Extract sample IDs from a VCF header

LIBRARY

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

SYNOPSIS

void    bl_vcf_get_sample_ids(FILE *vcf_stream, char *sample_ids[],
size_t first_col, size_t last_col)

ARGUMENTS

vcf_stream  FILE pointer to the VCF input stream
sample_ids  Array if character pointers to receive sample IDs
first_col   First column from which a sample ID should be saved
last_col    Last column from which a sample ID should be saved

DESCRIPTION

Extract sample IDs from a VCF input header line. This is typically done following bl_vcf_skip_meta_data(3), which will leave the FILE pointer pointing to the beginning of the header line, if one is present.

The arguments first_col and last_col represent the first and last sample columns, both inclusive, from which sample IDs should be extracted. A value of 1 represents the first sample column. This feature allows a VCF file with many columns to be processed in multiple stages. For example, the vcf-split tool, based on biolibc, cannot efficiently process more than abou1 10,000 samples at once, since each sample requires an open output file. A VCF with 150,000 samples can be processed in 15 separate passes.

SEE ALSO

bl_vcf_skip_meta_data(3)