recombinator.hpp File Reference

#include "gbwt_helper.hpp"
#include "gbwtgraph_helper.hpp"
#include "hash_map.hpp"
#include "snarl_distance_index.hpp"
#include <functional>
#include <iostream>
#include <gbwtgraph/algorithms.h>

Classes
class	vg::Haplotypes
struct	vg::Haplotypes::Header
	Header of the serialized file. More...
struct	vg::Haplotypes::Subchain
	Representation of a subchain. More...
struct	vg::Haplotypes::TopLevelChain
	Representation of a top-level chain. More...
class	vg::HaplotypePartitioner
struct	vg::HaplotypePartitioner::Subchain
struct	vg::HaplotypePartitioner::Parameters
	Parameters for partition_haplotypes(). More...
class	vg::Recombinator
struct	vg::Recombinator::Statistics
	Statistics on the generated haplotypes. More...
struct	vg::Recombinator::Parameters
	Parameters for generate_haplotypes(). More...
struct	vg::Recombinator::LocalHaplotype
	A local haplotype sequence within a single subchain. More...
struct	vg::PathPiece
	A maximal piece of a path whose nodes and edges all exist in a GBWT index. More...

Namespaces
	vg

Functions
std::vector< PathPiece >	vg::clip_path_to_index (const gbwt::vector_type &path, const gbwt::DynamicGBWT &index, const std::function< size_t(gbwt::node_type)> &node_length)

Detailed Description

Tools for generating synthetic haplotypes as recombinations of existing haplotypes.