bl_vcf_get_sample_ids(3) Library Functions Manual bl_vcf_get_sample_ids(3) 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) bl_vcf_get_sample_ids(3)
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