vg::Recombinator Class Reference

#include <recombinator.hpp>

Classes
struct	Statistics
	Statistics on the generated haplotypes. More...
struct	Parameters
	Parameters for generate_haplotypes(). More...
struct	LocalHaplotype
	A local haplotype sequence within a single subchain. More...

Public Types
enum	kmer_presence { absent , heterozygous , present , frequent }
	Kmer classification. More...
typedef Haplotypes::Verbosity	Verbosity
	The amount of progress information that should be printed to stderr.
typedef Haplotypes::sequence_type	sequence_type
	A GBWT sequence as (sequence identifier, offset in a node).

Public Member Functions
	Recombinator (const gbwtgraph::GBZ &gbz, const Haplotypes &haplotypes, Verbosity verbosity)
	Creates a new Recombinator.
gbwt::GBWT	generate_haplotypes (const std::string &kff_file, const Parameters &parameters) const

Public Attributes
const gbwtgraph::GBZ &	gbz
const Haplotypes &	haplotypes
gbwt::FragmentMap	fragment_map
Verbosity	verbosity
std::vector< size_t >	jobs_for_cached_paths

Static Public Attributes
static constexpr size_t	NUM_HAPLOTYPES = 4
	Number of haplotypes to be generated.
static constexpr size_t	NUM_CANDIDATES = 32
	A reasonable number of candidates for diploid sampling.
static constexpr double	BADNESS_THRESHOLD = 4.0
	Badness threshold for subchains.
static constexpr size_t	COVERAGE = 0
	Expected kmer coverage. Use 0 to estimate from kmer counts.
static constexpr size_t	KFF_BLOCK_SIZE = 1000000
	Block size (in kmers) for reading KFF files.
static constexpr double	PRESENT_DISCOUNT = 0.9
static constexpr double	HET_ADJUSTMENT = 0.05
static constexpr double	ABSENT_SCORE = 0.8
static constexpr size_t	MIN_GREF_LENGTH = 50

Private Member Functions
Statistics	generate_haplotypes (const Haplotypes::TopLevelChain &chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > &kmer_counts, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata, const Parameters &parameters, double coverage) const
Statistics	copy_chain (const Haplotypes::TopLevelChain &chain, gbwt::GBWTBuilder &builder, gbwtgraph::MetadataBuilder &metadata) const

Detailed Description

A class that creates synthetic haplotypes from a Haplotypes representation of local haplotypes.

Member Typedef Documentation

sequence_type

typedef Haplotypes::sequence_type vg::Recombinator::sequence_type

A GBWT sequence as (sequence identifier, offset in a node).

Verbosity

typedef Haplotypes::Verbosity vg::Recombinator::Verbosity

The amount of progress information that should be printed to stderr.

Member Enumeration Documentation

kmer_presence

enum vg::Recombinator::kmer_presence

Kmer classification.

Enumerator
absent
heterozygous
present
frequent

Constructor & Destructor Documentation

Recombinator()

vg::Recombinator::Recombinator	(	const gbwtgraph::GBZ &	gbz,
		const Haplotypes &	haplotypes,
		Verbosity	verbosity )

Creates a new Recombinator.

Member Function Documentation

copy_chain()

Recombinator::Statistics vg::Recombinator::copy_chain ( const Haplotypes::TopLevelChain & chain, gbwt::GBWTBuilder & builder, gbwtgraph::MetadataBuilder & metadata ) const

private

generate_haplotypes() [1/2]

Recombinator::Statistics vg::Recombinator::generate_haplotypes ( const Haplotypes::TopLevelChain & chain, const hash_map< Haplotypes::Subchain::kmer_type, size_t > & kmer_counts, gbwt::GBWTBuilder & builder, gbwtgraph::MetadataBuilder & metadata, const Parameters & parameters, double coverage ) const

private

generate_haplotypes() [2/2]

gbwt::GBWT vg::Recombinator::generate_haplotypes	(	const std::string &	kff_file,
		const Parameters &	parameters ) const

Generates haplotypes based on the kmer counts in the given KFF file.

Runs multiple GBWT construction jobs in parallel using OpenMP threads and generates the specified number of haplotypes in each top-level chain (component).

Each generated haplotype has a single source haplotype in each subchain. The source haplotype may consist of multiple fragments. Subchains are by unary paths. Suffix / prefix subchains in the middle of a chain create fragment breaks in every haplotype. If the chain starts without a prefix (ends without a suffix), the haplotype chosen for the first (last) subchain is used from the start (continued until the end).

Throws std::runtime_error on error in single-threaded parts and exits with std::exit(EXIT_FAILURE) in multi-threaded parts.

Member Data Documentation

ABSENT_SCORE

double vg::Recombinator::ABSENT_SCORE = 0.8

staticconstexpr

Score for getting an absent kmer right/wrong. This should be less than 1, if we assume that having the right variants in the graph is more important than keeping wrong variants out.

BADNESS_THRESHOLD

double vg::Recombinator::BADNESS_THRESHOLD = 4.0

staticconstexpr

Badness threshold for subchains.

COVERAGE

size_t vg::Recombinator::COVERAGE = 0

staticconstexpr

Expected kmer coverage. Use 0 to estimate from kmer counts.

fragment_map

gbwt::FragmentMap vg::Recombinator::fragment_map

gbz

const gbwtgraph::GBZ& vg::Recombinator::gbz

haplotypes

const Haplotypes& vg::Recombinator::haplotypes

HET_ADJUSTMENT

double vg::Recombinator::HET_ADJUSTMENT = 0.05

staticconstexpr

Adjustment to the score of a heterozygous kmer every time a haplotype with (-) or without (+) that kmer is selected.

jobs_for_cached_paths

std::vector<size_t> vg::Recombinator::jobs_for_cached_paths

KFF_BLOCK_SIZE

size_t vg::Recombinator::KFF_BLOCK_SIZE = 1000000

staticconstexpr

Block size (in kmers) for reading KFF files.

MIN_GREF_LENGTH

size_t vg::Recombinator::MIN_GREF_LENGTH = 50

staticconstexpr

Minimum length (in bp) for a piece of a gref fragment to survive in the sampled graph. The same floor as vg paths --min-gref-len.

NUM_CANDIDATES

size_t vg::Recombinator::NUM_CANDIDATES = 32

staticconstexpr

A reasonable number of candidates for diploid sampling.

NUM_HAPLOTYPES

size_t vg::Recombinator::NUM_HAPLOTYPES = 4

staticconstexpr

Number of haplotypes to be generated.

PRESENT_DISCOUNT

double vg::Recombinator::PRESENT_DISCOUNT = 0.9

staticconstexpr

Multiplier to the score of a present kmer every time a haplotype with that kmer is selected.

verbosity

Verbosity vg::Recombinator::verbosity

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The documentation for this class was generated from the following files:

• src/recombinator.hpp
• src/recombinator.cpp