#include <index_registry.hpp>

Public Member Functions
	IndexRegistry ()=default
	Constructor. More...

	~IndexRegistry ()
	Destructor to clean up temp files. More...

	IndexRegistry (const IndexRegistry &other)=delete

IndexRegistry &	operator= (const IndexRegistry &other)=delete

	IndexRegistry (IndexRegistry &&other)

IndexRegistry &	operator= (IndexRegistry &&other)

void	set_prefix (const string &prefix)
	Prefix for all saved outputs. More...

string	get_prefix () const
	Get the current prefix for saving output files. More...

void	set_intermediate_file_keeping (bool keep_intermediates)

void	register_index (const IndexName &identifier, const string &suffix)
	Register an index containing the given identifier. More...

void	register_index (const IndexName &identifier, const vector< string > &suffixes)

RecipeName	register_recipe (const vector< IndexName > &identifiers, const vector< IndexName > &input_identifiers, const RecipeFunc &exec)

void	register_generalization (const RecipeName &generalizer, const RecipeName &generalizee)

void	provide (const IndexName &identifier, const string &filename, const map< string, string > &scopes={})

void	provide (const IndexName &identifier, const vector< string > &filenames, const map< string, string > &scopes={})

void	reset (const IndexName &identifier)
	Remove a provided index. More...

bool	available (const IndexName &identifier) const

vector< string >	get_possible_filenames (const IndexName &identifier) const

vector< string >	require (const IndexName &identifier) const

void	set_target_memory_usage (int64_t bytes)

int64_t	get_target_memory_usage () const
	Get the maximum memory we will try to consume. More...

vector< IndexName >	completed_indexes () const
	Get a list of all indexes that have already been completed or provided. More...

void	make_indexes (const vector< IndexName > &identifiers)

string	to_dot () const
	Returns the recipe graph in dot format. More...

string	to_dot (const vector< IndexName > &targets) const
	Returns the recipe graph in dot format with a plan highlighted. More...

void	reset ()
	Discard any provided or constructed indexes. More...

Static Public Member Functions
static set< string >	get_wildcards (const string &pattern)
	Get the names of all brace-enclosed {wildcards} in the given pattern. More...

static string	substitute_wildcards (const string &pattern, const map< string, string > values)

static int64_t	get_system_memory ()
	Get the amount of free memory. More...

static bool	vcf_is_phased (const string &filepath)
	Determine if a VCF file is phased or not. More...

static bool	gfa_has_haplotypes (const string &filepath)
	Determine if a GFA has haplotypes as W-lines. More...

Public Attributes
bool	check_files = true

Protected Member Functions
vector< IndexGroup >	dependency_order () const
	get a topological ordering of all registered indexes in the dependency DAG More...

IndexingPlan	make_plan (const IndexGroup &end_products) const
	generate a plan to create the indexes More...

bool	has_recipe (const RecipeName &recipe_name) const

const IndexRecipe &	get_recipe (const RecipeName &recipe_name) const
	use a recipe identifier to get the recipe More...

vector< vector< string > >	execute_recipe (const RecipeName &recipe_name, const IndexingPlan *plan, AliasGraph &alias_graph)

IndexFile *	get_index (const IndexName &identifier)
	access index file More...

const IndexFile *	get_index (const IndexName &identifier) const
	access const index file More...

bool	all_finished (const vector< const IndexFile * > &inputs) const

bool	all_finished (const IndexGroup &inputs) const

string	get_work_dir ()
	Function to get and/or initialize the temporary directory in which indexes will live. More...

Protected Attributes
map< IndexName, unique_ptr< IndexFile > >	index_registry
	The storage struct for named indexes. Ordered so it is easier to key on index names. More...

unordered_set< string >	registered_suffixes
	All of the suffixes that have been registered by indexes. More...

map< IndexGroup, vector< IndexRecipe > >	recipe_registry
	The storage struct for recipes, which may make index. More...

map< RecipeName, RecipeName >	generalizations
	Map from generalizees to generalizers. More...

string	work_dir
	Temporary directory in which indexes will live. More...

string	output_prefix = "index"
	filepath that will prefix all saved output More...

bool	keep_intermediates = false
	should intermediate files end up in the scratch or the output directory? More...

int64_t	target_memory_usage = numeric_limits<int64_t>::max()
	the max memory we will attempt to use More...

Friends
class	IndexingPlan

Detailed Description

An object that can record methods to produce indexes and design workflows to create a set of desired indexes.

Constructor & Destructor Documentation

◆ IndexRegistry() [1/3]

vg::IndexRegistry::IndexRegistry ( )

default

Constructor.

◆ ~IndexRegistry()

vg::IndexRegistry::~IndexRegistry ( )

Destructor to clean up temp files.

◆ IndexRegistry() [2/3]

vg::IndexRegistry::IndexRegistry ( const IndexRegistry & other )

delete

◆ IndexRegistry() [3/3]

vg::IndexRegistry::IndexRegistry ( IndexRegistry && other )

Member Function Documentation

◆ all_finished() [1/2]

bool vg::IndexRegistry::all_finished ( const IndexGroup & inputs ) const

protected

◆ all_finished() [2/2]

bool vg::IndexRegistry::all_finished ( const vector< const IndexFile * > & inputs ) const

protected

◆ available()

bool vg::IndexRegistry::available ( const IndexName & identifier ) const

Return true if the given index is available and can be require()'d, and false otherwise.

◆ completed_indexes()

vector< IndexName > vg::IndexRegistry::completed_indexes ( ) const

Get a list of all indexes that have already been completed or provided.

◆ dependency_order()

vector< IndexGroup > vg::IndexRegistry::dependency_order ( ) const

protected

get a topological ordering of all registered indexes in the dependency DAG

◆ execute_recipe()

vector< vector< string > > vg::IndexRegistry::execute_recipe	(	const RecipeName &	recipe_name,
		const IndexingPlan *	plan,
		AliasGraph &	alias_graph
	)

protected

Build the index using the recipe with the provided priority. Expose the plan so that the recipe knows where it is supposed to go.

◆ get_index() [1/2]

IndexFile * vg::IndexRegistry::get_index ( const IndexName & identifier )

protected

access index file

◆ get_index() [2/2]

const IndexFile * vg::IndexRegistry::get_index ( const IndexName & identifier ) const

protected

access const index file

◆ get_possible_filenames()

vector< string > vg::IndexRegistry::get_possible_filenames ( const IndexName & identifier ) const

Get the possible filename(s) associated with the given index with the given prefix. TODO: Get this to account for sample-scoped indexes.

◆ get_prefix()

string vg::IndexRegistry::get_prefix ( ) const

Get the current prefix for saving output files.

◆ get_recipe()

const IndexRecipe & vg::IndexRegistry::get_recipe ( const RecipeName & recipe_name ) const

protected

use a recipe identifier to get the recipe

◆ get_system_memory()

int64_t vg::IndexRegistry::get_system_memory ( )

static

Get the amount of free memory.

◆ get_target_memory_usage()

int64_t vg::IndexRegistry::get_target_memory_usage ( ) const

Get the maximum memory we will try to consume.

◆ get_wildcards()

set< string > vg::IndexRegistry::get_wildcards ( const string & pattern )

static

Get the names of all brace-enclosed {wildcards} in the given pattern.

◆ get_work_dir()

string vg::IndexRegistry::get_work_dir ( )

protected

Function to get and/or initialize the temporary directory in which indexes will live.

◆ gfa_has_haplotypes()

bool vg::IndexRegistry::gfa_has_haplotypes ( const string & filepath )

static

Determine if a GFA has haplotypes as W-lines.

◆ has_recipe()

bool vg::IndexRegistry::has_recipe ( const RecipeName & recipe_name ) const

protected

Check if a recipe identifier correesponds to a recipe.

Recipe identifiers not corresponding to actual recipes are used during planning to represent provided inputs.

TODO: Refactor that with some kind of tagged union or optional.

◆ make_indexes()

void vg::IndexRegistry::make_indexes ( const vector< IndexName > & identifiers )

Create and execute a plan to make the indicated indexes using provided inputs If provided inputs cannot create the desired indexes, throws a InsufficientInputException. When completed, all requested index files will be available via require().

◆ make_plan()

IndexingPlan vg::IndexRegistry::make_plan ( const IndexGroup & end_products ) const

protected

generate a plan to create the indexes

◆ operator=() [1/2]

IndexRegistry& vg::IndexRegistry::operator= ( const IndexRegistry & other )

delete

◆ operator=() [2/2]

IndexRegistry & vg::IndexRegistry::operator= ( IndexRegistry && other )

◆ provide() [1/2]

void vg::IndexRegistry::provide	(	const IndexName &	identifier,
		const string &	filename,
		const map< string, string > &	scopes = `{}`
	)

Indicate a serialized file that contains some identified index, optionally with scopes that propagates to descendant files.

TODO: If scopes contain ".", we can run into problems with combinations of different scopes producing the same final string. Right now we only use one kind of scope, which avoids this.

◆ provide() [2/2]

void vg::IndexRegistry::provide	(	const IndexName &	identifier,
		const vector< string > &	filenames,
		const map< string, string > &	scopes = `{}`
	)

Indicate a list of serialized files that contains some identified index, optionally with scopes that propagates to descendant files.

TODO: If scopes contain ".", we can run into problems with combinations of different scopes producing the same final string. Right now we only use one kind of scope, which avoids this.

◆ register_generalization()

void vg::IndexRegistry::register_generalization	(	const RecipeName &	generalizer,
		const RecipeName &	generalizee
	)

Indicate one recipe is a broadened version of another. The indexes consumed and produced by the generalization must be semantically identical to those of the generalizee

◆ register_index() [1/2]

void vg::IndexRegistry::register_index	(	const IndexName &	identifier,
		const string &	suffix
	)

Register an index containing the given identifier.

◆ register_index() [2/2]

void vg::IndexRegistry::register_index	(	const IndexName &	identifier,
		const vector< string > &	suffixes
	)

Register an index containing the given identifier, with multiple possible suffixes. The first suffix where all {wildcards} can be substituted with scopes will be used.

◆ register_recipe()

RecipeName vg::IndexRegistry::register_recipe	(	const vector< IndexName > &	identifiers,
		const vector< IndexName > &	input_identifiers,
		const RecipeFunc &	exec
	)

Register a recipe to produce an index using other indexes or input files. Recipes registered earlier will have higher priority.

◆ require()

vector< string > vg::IndexRegistry::require ( const IndexName & identifier ) const

Get the filename(s) associated with the given index. Aborts if the index is not a known type, or if it is not provided or made.

◆ reset() [1/2]

void vg::IndexRegistry::reset ( )

Discard any provided or constructed indexes.

◆ reset() [2/2]

void vg::IndexRegistry::reset ( const IndexName & identifier )

Remove a provided index.

◆ set_intermediate_file_keeping()

void vg::IndexRegistry::set_intermediate_file_keeping ( bool keep_intermediates )

Should intermediate files be saved to the output directory or the temp directory?

◆ set_prefix()

void vg::IndexRegistry::set_prefix ( const string & prefix )

Prefix for all saved outputs.

◆ set_target_memory_usage()

void vg::IndexRegistry::set_target_memory_usage ( int64_t bytes )

Set the maximum memory that indexing should try to consume (note: this is not strictly adhered to due to difficulties in estimating memory use)

◆ substitute_wildcards()

string vg::IndexRegistry::substitute_wildcards	(	const string &	pattern,
		const map< string, string >	values
	)

static

Substitute wildcards into the given pattern. All wildcards must have values assigned. Extra values not used are allowed.

◆ to_dot() [1/2]

string vg::IndexRegistry::to_dot ( ) const

Returns the recipe graph in dot format.

◆ to_dot() [2/2]

string vg::IndexRegistry::to_dot ( const vector< IndexName > & targets ) const

Returns the recipe graph in dot format with a plan highlighted.

◆ vcf_is_phased()

bool vg::IndexRegistry::vcf_is_phased ( const string & filepath )

static

Determine if a VCF file is phased or not.

Friends And Related Function Documentation

◆ IndexingPlan

friend class IndexingPlan

friend

Member Data Documentation

◆ check_files

bool vg::IndexRegistry::check_files = true

◆ generalizations

map<RecipeName, RecipeName> vg::IndexRegistry::generalizations

protected

Map from generalizees to generalizers.

◆ index_registry

map<IndexName, unique_ptr<IndexFile> > vg::IndexRegistry::index_registry

protected

The storage struct for named indexes. Ordered so it is easier to key on index names.

◆ keep_intermediates

bool vg::IndexRegistry::keep_intermediates = false

protected

should intermediate files end up in the scratch or the output directory?

◆ output_prefix

string vg::IndexRegistry::output_prefix = "index"

protected

filepath that will prefix all saved output

◆ recipe_registry

map<IndexGroup, vector<IndexRecipe> > vg::IndexRegistry::recipe_registry

protected

The storage struct for recipes, which may make index.

◆ registered_suffixes

unordered_set<string> vg::IndexRegistry::registered_suffixes

protected

All of the suffixes that have been registered by indexes.

◆ target_memory_usage

int64_t vg::IndexRegistry::target_memory_usage = numeric_limits<int64_t>::max()

protected

the max memory we will attempt to use

◆ work_dir

string vg::IndexRegistry::work_dir

protected

Temporary directory in which indexes will live.

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

src/index_registry.hpp
src/index_registry.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ IndexRegistry() [1/3]

◆ ~IndexRegistry()

◆ IndexRegistry() [2/3]

◆ IndexRegistry() [3/3]

Member Function Documentation

◆ all_finished() [1/2]

◆ all_finished() [2/2]

◆ available()

◆ completed_indexes()

◆ dependency_order()

◆ execute_recipe()

◆ get_index() [1/2]

◆ get_index() [2/2]

◆ get_possible_filenames()

◆ get_prefix()

◆ get_recipe()

◆ get_system_memory()

◆ get_target_memory_usage()

◆ get_wildcards()

◆ get_work_dir()

◆ gfa_has_haplotypes()

◆ has_recipe()

◆ make_indexes()

◆ make_plan()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ provide() [1/2]

◆ provide() [2/2]

◆ register_generalization()

◆ register_index() [1/2]

◆ register_index() [2/2]

◆ register_recipe()

◆ require()

◆ reset() [1/2]

◆ reset() [2/2]

◆ set_intermediate_file_keeping()

◆ set_prefix()

◆ set_target_memory_usage()

◆ substitute_wildcards()

◆ to_dot() [1/2]

◆ to_dot() [2/2]

◆ vcf_is_phased()

Friends And Related Function Documentation

◆ IndexingPlan

Member Data Documentation

◆ check_files

◆ generalizations

◆ index_registry

◆ keep_intermediates

◆ output_prefix

◆ recipe_registry

◆ registered_suffixes

◆ target_memory_usage

◆ work_dir