vg::Haplotypes Class Reference

#include <recombinator.hpp>

Classes
struct	Header
	Header of the serialized file. More...
struct	Subchain
	Representation of a subchain. More...
struct	TopLevelChain
	Representation of a top-level chain. More...

Public Types
enum	Verbosity : size_t {   verbosity_silent = 0, verbosity_basic = 1, verbosity_detailed = 2, verbosity_debug = 3,   verbosity_extra_debug = 4 }
	The amount of progress information that should be printed to stderr. More...
typedef std::pair< gbwt::size_type, gbwt::size_type >	sequence_type
	A GBWT sequence as (sequence identifier, offset in a node). More...
typedef std::pair< std::uint32_t, std::uint32_t >	compact_sequence_type
	A more space-efficient representation of sequence_type. More...

Public Member Functions
size_t	components () const
	Returns the number of weakly connected components. More...
size_t	jobs () const
	Returns the number of GBWT construction jobs. More...
size_t	k () const
	Returns the length of the kmers. More...
size_t	kmers () const
	Returns the number of kmers in the subchains. More...
hash_map< Subchain::kmer_type, size_t >	kmer_counts (const std::string &kff_file, Verbosity verbosity) const
void	simple_sds_serialize (std::ostream &out) const
void	serialize_to (const std::string &filename) const
void	simple_sds_load (std::istream &in)
void	load_from (const std::string &filename)
size_t	simple_sds_size () const
	Returns the size of the object in elements. More...
std::vector< size_t >	assign_reference_paths (const gbwtgraph::GBZ &gbz, const gbwt::FragmentMap &fragment_map, Verbosity verbosity) const

Public Attributes
Header	header
std::vector< size_t >	jobs_for_cached_paths
std::vector< TopLevelChain >	chains

Detailed Description

A representation of the haplotypes in a graph.

The graph is partitioned into top-level chains, which are further partitioned into subchains. Each subchain contains a set of kmers and a collection of sequences. Each sequence is defined by a bitvector marking the kmers that are present.

At the moment, the kmers are minimizers with a single occurrence in the graph. The requirement is that each kmer is specific to a single subchain and does not occur anywhere else in either orientation. (If no haplotype crosses a snarl, that snarl is broken into a suffix and a prefix, and those subchains may share kmers.)

NOTE: This assumes that the top-level chains are linear, not cyclical.

Versions:

• Version 4: Subchains can have fragmented haplotypes instead of a single GBWT sequence always crossing from start to end. Compatible with version 3.
• Version 3: Subchains use smaller integers when possible. Compatible with version 2.
• Version 2: Top-level chains include a contig name. Compatible with version 1.
• Version 1: Initial version.

Member Typedef Documentation

compact_sequence_type

typedef std::pair<std::uint32_t, std::uint32_t> vg::Haplotypes::compact_sequence_type

A more space-efficient representation of sequence_type.

sequence_type

typedef std::pair<gbwt::size_type, gbwt::size_type> vg::Haplotypes::sequence_type

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

Member Enumeration Documentation

Verbosity

enum vg::Haplotypes::Verbosity : size_t

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

Enumerator
verbosity_silent	No progress information.
verbosity_basic	Basic information.
verbosity_detailed	Basic information and detailed statistics.
verbosity_debug	Basic information, detailed statistics, and debug information.
verbosity_extra_debug	Hidden level; potentially tens of thousands of lines of debugging information.

Member Function Documentation

assign_reference_paths()

std::vector< size_t > vg::Haplotypes::assign_reference_paths	(	const gbwtgraph::GBZ &	gbz,
		const gbwt::FragmentMap &	fragment_map,
		Verbosity	verbosity
	)		const

Assigns each reference and generic path in the graph to a GBWT construction job.

For each path handle from 0 to gbz.named_paths() - 1, we assign the path to the given construction job, or jobs() if the path is empty.

components()

size_t vg::Haplotypes::components ( ) const

inline

Returns the number of weakly connected components.

jobs()

size_t vg::Haplotypes::jobs ( ) const

inline

Returns the number of GBWT construction jobs.

k()

size_t vg::Haplotypes::k ( ) const

inline

Returns the length of the kmers.

kmer_counts()

hash_map< Haplotypes::Subchain::kmer_type, size_t > vg::Haplotypes::kmer_counts	(	const std::string &	kff_file,
		Verbosity	verbosity
	)		const

Returns a mapping from kmers to their counts in the given KFF file. The counts include both the kmer and the reverse complement.

Reads the KFF file using OpenMP threads. Exits with std::exit() if the file cannot be opened and throws std::runtime_error if the kmer counts cannot be used.

kmers()

size_t vg::Haplotypes::kmers ( ) const

inline

Returns the number of kmers in the subchains.

load_from()

void vg::Haplotypes::load_from

(

const std::string &

filename

)

Loads the object from a file in the Simple-SDS format. Prints an error message and exits the program on failure.

serialize_to()

void vg::Haplotypes::serialize_to

(

const std::string &

filename

)

const

Serializes the object to a file in the Simple-SDS format. Prints an error message and exits the program on failure.

simple_sds_load()

void vg::Haplotypes::simple_sds_load

(

std::istream &

in

)

Loads the object from a stream in the Simple-SDS format. I/O errors can be detected by checking the stream state. Throws sdsl::simple_sds::InvalidData if sanity checks fail.

simple_sds_serialize()

void vg::Haplotypes::simple_sds_serialize

(

std::ostream &

out

)

const

Serializes the object to a stream in the Simple-SDS format. I/O errors can be detected by checking the stream state.

simple_sds_size()

size_t vg::Haplotypes::simple_sds_size

(

)

const

Returns the size of the object in elements.

Member Data Documentation

chains

std::vector<TopLevelChain> vg::Haplotypes::chains

header

Header vg::Haplotypes::header

jobs_for_cached_paths

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

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

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