#include <genesis/population/stream/variant_input_stream_sources.hpp>

Detailed Description

Parameters to use when streaming through a VCF file as Variants.

This is used in make_variant_input_stream_from_pool_vcf_file() and make_variant_input_stream_from_individual_vcf_file() to set the paramters for the reading and conversion to Variant.

If only_snps is set, only SNP records are processed; that is, all non-SNPs (indels and others) are ignored. If only_biallelic_snps is set to true, this is further restricted to only contain biallelic SNPs, that is, only positions with exactly one alternative allele.

If only_filter_pass is set to true, only those positions are considered that have the FILTER field set to "PASS" (or missing "."). That is, all variants that did not pass a filter in the VCF processing are skipped. If only_filter_pass is set to false however (default), these position are used, but the VariantFilterTag::kNotPassed is set to indicate the failing filter.

The list of sample_names is used as a filter so that only those samples (columns of the VCF records) are evaluated and accessible - or, if inverse_sample_names is set to true, instead all but those samples.

Definition at line 253 of file variant_input_stream_sources.hpp.

Public Attributes
bool	inverse_sample_names = false

bool	only_biallelic_snps = false

bool	only_filter_pass = false

bool	only_snps = false

std::vector< std::string >	sample_names