variant_input_iterator.hpp File Reference

#include "genesis/population/formats/sam_variant_input_iterator.hpp"
#include "genesis/population/formats/simple_pileup_input_iterator.hpp"
#include "genesis/population/formats/sync_input_iterator.hpp"
#include "genesis/population/formats/sync_reader.hpp"
#include "genesis/population/formats/vcf_input_iterator.hpp"
#include "genesis/population/base_counts.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/utils/containers/lambda_iterator.hpp"
#include <cassert>
#include <functional>
#include <stdexcept>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
struct	VariantInputIteratorData
	Data storage for input-specific information when traversing a variant file. More...

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Typedefs
using	VariantInputIterator = utils::LambdaIterator< Variant, VariantInputIteratorData >
	Iterate Variants, using a variety of input file formats. More...

Functions
VariantInputIterator	make_variant_input_iterator_from_individual_vcf_file (std::string const &filename, bool use_allelic_depth=false, bool only_biallelic=true, bool only_filter_pass=true)
	Create a VariantInputIterator to iterate the contents of a VCF file as Variants, treating each sample as an individual, and combining them all into one BaseCounts sample. More...
VariantInputIterator	make_variant_input_iterator_from_individual_vcf_file (std::string const &filename, std::vector< std::string > const &sample_names, bool inverse_sample_names=false, bool use_allelic_depth=false, bool only_biallelic=true, bool only_filter_pass=true)
	Create a VariantInputIterator to iterate the contents of a VCF file as Variants, treating each sample as an individual, and combining them all into one BaseCounts sample. More...
VariantInputIterator	make_variant_input_iterator_from_pileup_file (std::string const &filename, SimplePileupReader const &reader=SimplePileupReader{})
	Create a VariantInputIterator to iterate the contents of a (m)pileup file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_pileup_file (std::string const &filename, std::vector< bool > const &sample_filter, SimplePileupReader const &reader=SimplePileupReader{})
	Create a VariantInputIterator to iterate the contents of a (m)pileup file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_pileup_file (std::string const &filename, std::vector< size_t > const &sample_indices, bool inverse_sample_indices=false, SimplePileupReader const &reader=SimplePileupReader{})
	Create a VariantInputIterator to iterate the contents of a (m)pileup file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_pool_vcf_file (std::string const &filename, bool only_biallelic=true, bool only_filter_pass=true)
	Create a VariantInputIterator to iterate the contents of a VCF file as Variants, treating each sample as a pool of individuals. More...
VariantInputIterator	make_variant_input_iterator_from_pool_vcf_file (std::string const &filename, std::vector< std::string > const &sample_names, bool inverse_sample_names=false, bool only_biallelic=true, bool only_filter_pass=true)
	Create a VariantInputIterator to iterate the contents of a VCF file as Variants, treating each sample as a pool of individuals. More...
VariantInputIterator	make_variant_input_iterator_from_sam_file (std::string const &filename, SamVariantInputIterator const &reader=SamVariantInputIterator{})
	Create a VariantInputIterator to iterate the contents of a SAM/BAM/CRAM file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_sync_file (std::string const &filename)
	Create a VariantInputIterator to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_sync_file (std::string const &filename, std::vector< bool > const &sample_filter)
	Create a VariantInputIterator to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_sync_file (std::string const &filename, std::vector< size_t > const &sample_indices, bool inverse_sample_indices=false)
	Create a VariantInputIterator to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputIterator	make_variant_input_iterator_from_variant_parallel_input_iterator (VariantParallelInputIterator const &parallel_input, bool allow_ref_base_mismatches=false, bool allow_alt_base_mismatches=true, std::string const &source_sample_separator=":")
	Create a VariantInputIterator to iterate multiple input sources at once, using a VariantParallelInputIterator. More...