variant_input_stream_adapters.cpp File Reference

#include "genesis/population/stream/variant_input_stream_adapters.hpp"
#include "genesis/population/filter/sample_counts_filter.hpp"
#include "genesis/population/filter/variant_filter.hpp"
#include "genesis/population/function/functions.hpp"
#include "genesis/utils/core/fs.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/text/string.hpp"
#include <algorithm>
#include <cassert>
#include <cstdint>
#include <memory>
#include <stdexcept>
#include <unordered_set>
#include <utility>

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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_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...
VariantMergeGroupAssignment	make_variant_merging_input_stream_group_assignment_ (VariantInputStream const &variant_input, std::unordered_map< std::string, std::string > const &sample_name_to_group, bool allow_ungrouped_samples)
	Helper function to create a mapping from sample indices to group indices. More...