handlegraph::PathMetadata Class Reference

#include <path_metadata.hpp>

Inheritance diagram for handlegraph::PathMetadata:

Public Member Functions
virtual	~PathMetadata ()=default
virtual PathSense	get_sense (const path_handle_t &handle) const
	What is the given path meant to be representing? More...
virtual std::string	get_sample_name (const path_handle_t &handle) const
virtual std::string	get_locus_name (const path_handle_t &handle) const
virtual size_t	get_haplotype (const path_handle_t &handle) const
virtual size_t	get_phase_block (const path_handle_t &handle) const
virtual subrange_t	get_subrange (const path_handle_t &handle) const
template<typename Iteratee >
bool	for_each_path_of_sense (const PathSense &sense, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_path_of_sense (const std::unordered_set< PathSense > &senses, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_path_of_sample (const std::string &sample, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_path_of_sample (const std::unordered_set< std::string > &samples, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_step_of_sense (const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const
template<typename Iteratee >
bool	for_each_step_of_sense (const handle_t &visited, const std::unordered_set< PathSense > &senses, const Iteratee &iteratee) const

Static Public Member Functions
static PathSense	parse_sense (const std::string &path_name)
static std::string	parse_sample_name (const std::string &path_name)
static std::string	parse_locus_name (const std::string &path_name)
static size_t	parse_haplotype (const std::string &path_name)
static size_t	parse_phase_block (const std::string &path_name)
static subrange_t	parse_subrange (const std::string &path_name)
static void	parse_path_name (const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange)
	Decompose a formatted path name into metadata. More...
static std::string	create_path_name (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange)

Static Public Attributes
static const std::string	NO_SAMPLE_NAME = ""
static const std::string	NO_LOCUS_NAME = ""
static const size_t	NO_HAPLOTYPE = std::numeric_limits<size_t>::max()
static const size_t	NO_PHASE_BLOCK = std::numeric_limits<size_t>::max()
static const subrange_t	NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION}
static const offset_t	NO_END_POSITION = std::numeric_limits<offset_t>::max()

Protected Member Functions
virtual bool	for_each_path_matching_impl (const std::unordered_set< PathSense > *senses, const std::unordered_set< std::string > *samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) const
virtual bool	for_each_step_of_sense_impl (const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const
virtual bool	for_each_step_of_sense_impl (const handle_t &visited, const std::unordered_set< PathSense > &senses, const std::function< bool(const step_handle_t &)> &iteratee) const
virtual std::string	get_path_name (const path_handle_t &path_handle) const =0
	Look up the name of a path from a handle to it. More...
virtual path_handle_t	get_path_handle_of_step (const step_handle_t &step_handle) const =0
	Returns a handle to the path that an step is on. More...
virtual bool	for_each_path_handle_impl (const std::function< bool(const path_handle_t &)> &iteratee) const =0
virtual bool	for_each_step_on_handle_impl (const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0

Static Private Attributes
static const std::regex	FORMAT
static const size_t	ASSEMBLY_OR_NAME_MATCH = 1
static const size_t	LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE = 2
static const size_t	HAPLOTYPE_MATCH = 2
static const size_t	LOCUS_MATCH_ANY = 3
static const size_t	PHASE_BLOCK_MATCH = 4
static const size_t	RANGE_START_MATCH = 5
static const size_t	RANGE_END_MATCH = 6
static const char	SEPARATOR = '#'
	Separator used to separate path name components. More...
static const char	RANGE_START_SEPARATOR = '['
static const char	RANGE_END_SEPARATOR = '-'
static const char	RANGE_TERMINATOR = ']'

Detailed Description

This is the interface for embedded path and haplotype thread metadata.

Comes with a default implementation of this interface, based on a get_path_name() and special path name formatting.

Our model is that paths come in different "senses":

• SENSE_GENERIC: a generic named path. Has a "locus" name.
• SENSE_REFERENCE: a part of a reference assembly. Has a "sample" name, a "locus" name, and a haplotype number.
• SENSE_HAPLOTYPE: a haplotype from a particular individual. Has a "sample" name, a "locus" name, a haplotype number, and a phase block identifier.

Paths of all sneses can represent subpaths, with bounds.

Depending on sense, a path might have:

• Sample: sample or assembly name.
• Locus: contig, scaffold, or gene name path either represents in its assembly or is an allele of in its sample.
• Haplotype number: number identifying which haplotype of a locus is being represented. GFA uses a convention where the presence of a haplotype 0 implies that only one haplotype is present.
• Phase block identifier: Distinguishes fragments of a haplotype that are phased but not necessarily part of a single self-consistent scaffold (often due to self-contradictory VCF information). Must be unique within a sample, locus, and haplotype. May be a number or a start coordinate.
• Bounds, for when a path as stored gives only a sub-range of a conceptually longer path. Multiple items can be stored with identical metadata in the other fields if their bounds are non-overlapping. TODO: Interaction with phase block in GBWT???

Constructor & Destructor Documentation

~PathMetadata()

virtual handlegraph::PathMetadata::~PathMetadata ( )

virtualdefault

Member Function Documentation

create_path_name()

std::string handlegraph::PathMetadata::create_path_name ( const PathSense &  sense, const std::string &  sample, const std::string &  locus, const size_t &  haplotype, const size_t &  phase_block, const subrange_t &  subrange  )

static

Compose a formatted path name for the given metadata. Any item can be the corresponding unset sentinel (PathMetadata::NO_LOCUS_NAME, PathMetadata::NO_PHASE_BLOCK, etc.).

for_each_path_handle_impl()

virtual bool handlegraph::PathMetadata::for_each_path_handle_impl ( const std::function< bool(const path_handle_t &)> &  iteratee ) const

protectedpure virtual

Execute a function on each path in the graph. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.

Implemented in handlegraph::PathHandleGraph, vg::PathSubgraphOverlay, vg::MemoizingGraph, and xg::XG.

for_each_path_matching() [1/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_matching	(	const std::unordered_set< PathSense > &	senses,
		const std::unordered_set< std::string > &	samples,
		const std::unordered_set< std::string > &	loci,
		const Iteratee &	iteratee
	)		const

Loop through all the paths matching the given query. Query elements which are empty match everything. Returns false and stops if the iteratee returns false.

for_each_path_matching() [2/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_matching	(	const std::unordered_set< PathSense > *	senses,
		const std::unordered_set< std::string > *	samples,
		const std::unordered_set< std::string > *	loci,
		const Iteratee &	iteratee
	)		const

Loop through all the paths matching the given query. Query elements which are null match everything. Returns false and stops if the iteratee returns false.

for_each_path_matching_impl()

bool handlegraph::PathMetadata::for_each_path_matching_impl ( const std::unordered_set< PathSense > *  senses, const std::unordered_set< std::string > *  samples, const std::unordered_set< std::string > *  loci, const std::function< bool(const path_handle_t &)> &  iteratee  ) const

protectedvirtual

Loop through all the paths matching the given query. Query elements which are null match everything. Returns false and stops if the iteratee returns false.

for_each_path_of_sample() [1/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_of_sample	(	const std::string &	sample,
		const Iteratee &	iteratee
	)		const

Loop through all the paths with the given sample name. Returns false and stops if the iteratee returns false.

for_each_path_of_sample() [2/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_of_sample	(	const std::unordered_set< std::string > &	samples,
		const Iteratee &	iteratee
	)		const

Loop through all the paths with any of the given sample names. Returns false and stops if the iteratee returns false.

for_each_path_of_sense() [1/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_of_sense	(	const PathSense &	sense,
		const Iteratee &	iteratee
	)		const

Loop through all the paths with the given sense. Returns false and stops if the iteratee returns false.

for_each_path_of_sense() [2/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_path_of_sense	(	const std::unordered_set< PathSense > &	senses,
		const Iteratee &	iteratee
	)		const

Loop through all the paths with any of the given senses. Returns false and stops if the iteratee returns false.

for_each_step_of_sense() [1/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_step_of_sense	(	const handle_t &	visited,
		const PathSense &	sense,
		const Iteratee &	iteratee
	)		const

Loop through all steps on the given handle for paths with the given sense. Returns false and stops if the iteratee returns false. TODO: Take the opportunity to make steps track orientation better?

for_each_step_of_sense() [2/2]

template<typename Iteratee >

bool handlegraph::PathMetadata::for_each_step_of_sense	(	const handle_t &	visited,
		const std::unordered_set< PathSense > &	senses,
		const Iteratee &	iteratee
	)		const

Loop through all steps on the given handle for paths with any of the given senses. Returns false and stops if the iteratee returns false.

for_each_step_of_sense_impl() [1/2]

bool handlegraph::PathMetadata::for_each_step_of_sense_impl ( const handle_t &  visited, const PathSense &  sense, const std::function< bool(const step_handle_t &)> &  iteratee  ) const

protectedvirtual

Loop through all steps on the given handle for paths with the given sense. Returns false and stops if the iteratee returns false.

for_each_step_of_sense_impl() [2/2]

bool handlegraph::PathMetadata::for_each_step_of_sense_impl ( const handle_t &  visited, const std::unordered_set< PathSense > &  senses, const std::function< bool(const step_handle_t &)> &  iteratee  ) const

protectedvirtual

Loop through all steps on the given handle for paths with any of the given senses. Returns false and stops if the iteratee returns false.

for_each_step_on_handle_impl()

virtual bool handlegraph::PathMetadata::for_each_step_on_handle_impl ( const handle_t &  handle, const std::function< bool(const step_handle_t &)> &  iteratee  ) const

protectedpure virtual

Execute a function on each step of a handle in any path. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.

Implemented in handlegraph::PathHandleGraph, vg::PathSubgraphOverlay, vg::MemoizingGraph, and xg::XG.

get_haplotype()

size_t handlegraph::PathMetadata::get_haplotype ( const path_handle_t &  handle ) const

virtual

Get the haplotype number (0 or 1, for diploid) of the path-or-thread, or NO_HAPLOTYPE if it does not belong to one.

get_locus_name()

std::string handlegraph::PathMetadata::get_locus_name ( const path_handle_t &  handle ) const

virtual

Get the name of the contig or gene asociated with the path-or-thread, or NO_LOCUS_NAME if it does not belong to one.

get_path_handle_of_step()

virtual path_handle_t handlegraph::PathMetadata::get_path_handle_of_step ( const step_handle_t &  step_handle ) const

protectedpure virtual

Returns a handle to the path that an step is on.

Implemented in handlegraph::PathHandleGraph, vg::VG, vg::PathSubgraphOverlay, vg::MemoizingGraph, and xg::XG.

get_path_name()

virtual std::string handlegraph::PathMetadata::get_path_name ( const path_handle_t &  path_handle ) const

protectedpure virtual

Look up the name of a path from a handle to it.

Implemented in handlegraph::PathHandleGraph, vg::VG, vg::PathSubgraphOverlay, vg::MemoizingGraph, and xg::XG.

get_phase_block()

size_t handlegraph::PathMetadata::get_phase_block ( const path_handle_t &  handle ) const

virtual

Get the phase block number (contiguously phased region of a sample, contig, and haplotype) of the path-or-thread, or NO_PHASE_BLOCK if it does not belong to one.

get_sample_name()

std::string handlegraph::PathMetadata::get_sample_name ( const path_handle_t &  handle ) const

virtual

Get the name of the sample or assembly asociated with the path-or-thread, or NO_SAMPLE_NAME if it does not belong to one.

get_sense()

PathSense handlegraph::PathMetadata::get_sense ( const path_handle_t &  handle ) const

virtual

What is the given path meant to be representing?

get_subrange()

subrange_t handlegraph::PathMetadata::get_subrange ( const path_handle_t &  handle ) const

virtual

Get the bounds of the path-or-thread that are actually represented here. Should be NO_SUBRANGE if the entirety is represented here, and 0-based inclusive start and exclusive end positions of the stored region on the full path-or-thread if a subregion is stored.

If no end position is stored, NO_END_POSITION may be returned for the end position.

parse_haplotype()

size_t handlegraph::PathMetadata::parse_haplotype ( const std::string &  path_name )

static

Get the haplotype number (0 or 1, for diploid) embedded in the given formatted path name, or NO_HAPLOTYPE if it does not belong to one.

parse_locus_name()

std::string handlegraph::PathMetadata::parse_locus_name ( const std::string &  path_name )

static

Get the name of the contig or gene embedded in the given formatted path name, or NO_LOCUS_NAME if it does not belong to one.

parse_path_name()

void handlegraph::PathMetadata::parse_path_name ( const std::string &  path_name, PathSense &  sense, std::string &  sample, std::string &  locus, size_t &  haplotype, size_t &  phase_block, subrange_t &  subrange  )

static

Decompose a formatted path name into metadata.

parse_phase_block()

size_t handlegraph::PathMetadata::parse_phase_block ( const std::string &  path_name )

static

Get the phase block number (contiguously phased region of a sample, contig, and haplotype) embedded in the given formatted path name, or NO_PHASE_BLOCK if it does not belong to one.

parse_sample_name()

std::string handlegraph::PathMetadata::parse_sample_name ( const std::string &  path_name )

static

Get the name of the sample or assembly embedded in the given formatted path name, or NO_SAMPLE_NAME if it does not belong to one.

parse_sense()

PathSense handlegraph::PathMetadata::parse_sense ( const std::string &  path_name )

static

Extract the sense of a path from the given formatted path name, if possible. If not possible, return SENSE_GENERIC.

parse_subrange()

subrange_t handlegraph::PathMetadata::parse_subrange ( const std::string &  path_name )

static

Get the bounds embedded in the given formatted path name, or NO_SUBRANGE if they are absent. If no end position is stored, NO_END_POSITION may be returned for the end position.

Member Data Documentation

ASSEMBLY_OR_NAME_MATCH

const size_t handlegraph::PathMetadata::ASSEMBLY_OR_NAME_MATCH = 1

staticprivate

FORMAT

const std::regex handlegraph::PathMetadata::FORMAT

staticprivate

HAPLOTYPE_MATCH

const size_t handlegraph::PathMetadata::HAPLOTYPE_MATCH = 2

staticprivate

LOCUS_MATCH_ANY

const size_t handlegraph::PathMetadata::LOCUS_MATCH_ANY = 3

staticprivate

LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE

const size_t handlegraph::PathMetadata::LOCUS_MATCH_NUMERICAL_WITHOUT_HAPLOTYPE = 2

staticprivate

NO_END_POSITION

const offset_t handlegraph::PathMetadata::NO_END_POSITION = std::numeric_limits<offset_t>::max()

static

NO_HAPLOTYPE

const size_t handlegraph::PathMetadata::NO_HAPLOTYPE = std::numeric_limits<size_t>::max()

static

NO_LOCUS_NAME

const std::string handlegraph::PathMetadata::NO_LOCUS_NAME = ""

static

NO_PHASE_BLOCK

const size_t handlegraph::PathMetadata::NO_PHASE_BLOCK = std::numeric_limits<size_t>::max()

static

NO_SAMPLE_NAME

const std::string handlegraph::PathMetadata::NO_SAMPLE_NAME = ""

static

NO_SUBRANGE

const subrange_t handlegraph::PathMetadata::NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION}

static

PHASE_BLOCK_MATCH

const size_t handlegraph::PathMetadata::PHASE_BLOCK_MATCH = 4

staticprivate

RANGE_END_MATCH

const size_t handlegraph::PathMetadata::RANGE_END_MATCH = 6

staticprivate

RANGE_END_SEPARATOR

const char handlegraph::PathMetadata::RANGE_END_SEPARATOR = '-'

staticprivate

RANGE_START_MATCH

const size_t handlegraph::PathMetadata::RANGE_START_MATCH = 5

staticprivate

RANGE_START_SEPARATOR

const char handlegraph::PathMetadata::RANGE_START_SEPARATOR = '['

staticprivate

RANGE_TERMINATOR

const char handlegraph::PathMetadata::RANGE_TERMINATOR = ']'

staticprivate

SEPARATOR

const char handlegraph::PathMetadata::SEPARATOR = '#'

staticprivate

Separator used to separate path name components.

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

• deps/libhandlegraph/src/include/handlegraph/path_metadata.hpp
• deps/libhandlegraph/src/path_metadata.cpp