recombinator.cpp File Reference

#include "recombinator.hpp"
#include "kff.hpp"
#include "statistics.hpp"
#include "algorithms/component.hpp"
#include <algorithm>
#include <cmath>
#include <map>

Classes
struct	vg::RecombinatorHaplotype

Namespaces
	vg

Functions
std::string	vg::to_string (handle_t handle)
hash_map< Haplotypes::Subchain::kmer_type, size_t >::iterator	vg::find_kmer (hash_map< Haplotypes::Subchain::kmer_type, size_t > &counts, Haplotypes::Subchain::kmer_type kmer, size_t k)
void	vg::sa_to_da (std::vector< HaplotypePartitioner::sequence_type > &sequences, const gbwt::FastLocate &r_index)
std::string	vg::generate_haplotype (gbwt::edge_type pos, handle_t end, size_t start_max, size_t end_max, const gbwtgraph::GBWTGraph &graph)
std::vector< HaplotypePartitioner::kmer_type >	vg::take_unique_minimizers (const std::string &sequence, const HaplotypePartitioner::minimizer_index_type &minimizer_index)
void	vg::present_kmers (const std::vector< std::vector< HaplotypePartitioner::kmer_type >> &sequences, std::vector< std::pair< HaplotypePartitioner::kmer_type, size_t >> &all_kmers, sdsl::bit_vector &kmers_present)
void	vg::add_path (const gbwt::GBWT &source, gbwt::size_type path_id, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata)
void	vg::recombinator_sanity_checks (const Recombinator::Parameters &parameters)
double	vg::get_or_estimate_coverage (const hash_map< Haplotypes::Subchain::kmer_type, size_t > &counts, const Recombinator::Parameters &parameters, Haplotypes::Verbosity verbosity)
std::vector< std::pair< Recombinator::kmer_presence, double > >	vg::classify_kmers (const Haplotypes::Subchain &subchain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, double coverage, Recombinator::Statistics *statistics, const Recombinator::Parameters &parameters)
std::vector< std::pair< size_t, double > >	vg::select_diploid (const Haplotypes::Subchain &subchain, const std::vector< std::pair< size_t, double >> &candidates, const std::vector< std::pair< Recombinator::kmer_presence, double >> &kmer_types)
std::vector< std::pair< size_t, double > >	vg::select_haplotypes (const Haplotypes::Subchain &subchain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, double coverage, Recombinator::Statistics *statistics, std::vector< Recombinator::LocalHaplotype > *local_haplotypes, const Recombinator::Parameters &parameters)