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| bl_vcf_get_sample_ids(3) | FreeBSD Library Functions Manual | bl_vcf_get_sample_ids(3) |
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_header(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_header(3)
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