variant_input_stream_adapters.hpp File Reference

#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/sample_counts.hpp"
#include "genesis/population/stream/variant_gapless_input_stream.hpp"
#include "genesis/population/stream/variant_input_stream_sources.hpp"
#include "genesis/population/stream/variant_input_stream.hpp"
#include "genesis/population/stream/variant_parallel_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.

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_gapless_input_stream (VariantInputStream const &input)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_gapless_input_stream (VariantInputStream const &input, std::shared_ptr< GenomeLocusSet > genome_locus_set)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_gapless_input_stream (VariantInputStream const &input, std::shared_ptr<::genesis::sequence::ReferenceGenome > ref_genome)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_gapless_input_stream (VariantInputStream const &input, std::shared_ptr<::genesis::sequence::ReferenceGenome > ref_genome, std::shared_ptr< GenomeLocusSet > genome_locus_set)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_gapless_input_stream (VariantInputStream const &input, std::shared_ptr<::genesis::sequence::SequenceDict > seq_dict)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_gapless_input_stream (VariantInputStream const &input, std::shared_ptr<::genesis::sequence::SequenceDict > seq_dict, std::shared_ptr< GenomeLocusSet > genome_locus_set)
	Create a VariantGaplessInputStream from a VariantInputStream input, and wrap it agian in a VariantInputStream. More...
VariantInputStream	make_variant_input_stream_from_variant_gapless_input_stream (VariantGaplessInputStream const &gapless_input)
	Create a VariantInputStream that wraps a VariantGaplessInputStream. More...
VariantInputStream	make_variant_input_stream_from_variant_parallel_input_stream (VariantParallelInputStream const &parallel_input, VariantParallelInputStream::JoinedVariantParams const &joined_variant_params=VariantParallelInputStream::JoinedVariantParams{})
	Create a VariantInputStream to iterate multiple input sources at once, using a VariantParallelInputStream. More...
VariantInputStream	make_variant_merging_input_stream (VariantInputStream const &input, std::unordered_map< std::string, std::string > const &sample_name_to_group, bool allow_ungrouped_samples=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Create a VariantInputStream that merges samples from its underlying input. More...