variant_input_stream_sources.hpp File Reference

#include "genesis/population/format/frequency_table_input_stream.hpp"
#include "genesis/population/format/sam_variant_input_stream.hpp"
#include "genesis/population/format/simple_pileup_input_stream.hpp"
#include "genesis/population/format/sync_input_stream.hpp"
#include "genesis/population/format/sync_reader.hpp"
#include "genesis/population/format/vcf_input_stream.hpp"
#include "genesis/population/sample_counts.hpp"
#include "genesis/population/stream/variant_input_stream.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/sequence/reference_genome.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/utils/containers/generic_input_stream.hpp"
#include <cassert>
#include <functional>
#include <stdexcept>
#include <string>
#include <unordered_map>
#include <vector>

Go to the source code of this file.

Classes
struct	VariantInputStreamFromVcfParams
	Parameters to use when streaming through a VCF file as Variants. More...

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

Functions
VariantInputStream	make_variant_input_stream_from_frequency_table_file (std::string const &filename, char separator_char='\t', FrequencyTableInputStream const &reader=FrequencyTableInputStream{})
	Create a VariantInputStream to iterate the contents of a frequency table file as Variants. More...
VariantInputStream	make_variant_input_stream_from_frequency_table_file (std::string const &filename, std::vector< std::string > const &sample_names_filter, bool inverse_sample_names_filter=false, char separator_char='\t', FrequencyTableInputStream const &reader=FrequencyTableInputStream{})
	Create a VariantInputStream to iterate the contents of a frequency table file as Variants. More...
VariantInputStream	make_variant_input_stream_from_individual_vcf_file (std::string const &filename, VariantInputStreamFromVcfParams const &params=VariantInputStreamFromVcfParams{}, bool use_allelic_depth=false)
	Create a VariantInputStream to iterate the contents of a VCF file as Variants, treating each sample as an individual, and combining them all into one SampleCounts sample. More...
VariantInputStream	make_variant_input_stream_from_pileup_file (std::string const &filename, SimplePileupReader const &reader=SimplePileupReader{})
	Create a VariantInputStream to iterate the contents of a (m)pileup file as Variants. More...
VariantInputStream	make_variant_input_stream_from_pileup_file (std::string const &filename, std::vector< bool > const &sample_filter, SimplePileupReader const &reader=SimplePileupReader{})
	Create a VariantInputStream to iterate the contents of a (m)pileup file as Variants. More...
VariantInputStream	make_variant_input_stream_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 VariantInputStream to iterate the contents of a (m)pileup file as Variants. More...
VariantInputStream	make_variant_input_stream_from_pool_vcf_file (std::string const &filename, VariantInputStreamFromVcfParams const &params=VariantInputStreamFromVcfParams{})
	Create a VariantInputStream to iterate the contents of a VCF file as Variants, treating each sample as a pool of individuals. More...
VariantInputStream	make_variant_input_stream_from_sam_file (std::string const &filename, SamVariantInputStream const &reader=SamVariantInputStream{})
	Create a VariantInputStream to iterate the contents of a SAM/BAM/CRAM file as Variants. More...
VariantInputStream	make_variant_input_stream_from_sync_file (std::string const &filename)
	Create a VariantInputStream to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputStream	make_variant_input_stream_from_sync_file (std::string const &filename, std::vector< bool > const &sample_filter)
	Create a VariantInputStream to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputStream	make_variant_input_stream_from_sync_file (std::string const &filename, std::vector< size_t > const &sample_indices, bool inverse_sample_indices=false)
	Create a VariantInputStream to iterate the contents of a PoPoolation2 sync file as Variants. More...
VariantInputStream	make_variant_input_stream_from_vector (std::vector< Variant > const &variants)
	Create a VariantInputStream to iterate the contents of std::vector containing Variants. More...