#include <banded_global_aligner.hpp>

Classes
class	Deflection

Public Member Functions
	AltTracebackStack (const HandleGraph &graph, int64_t max_multi_alns, int32_t empty_score, unordered_set< BAMatrix * > &source_node_matrices, unordered_set< BAMatrix * > &sink_node_matrices, int8_t gap_open, int8_t gap_extend, IntType min_inf)

	~AltTracebackStack ()

void	get_alignment_start (int64_t &node_id, matrix_t &matrix)
	Get the start position of the current alignment and advance deflection pointer to the first deflection. More...

bool	has_next ()
	Are there any more alternate alignments in the stack? More...

void	next_traceback_alignment ()
	Advance to the next alternate trac. More...

bool	next_is_empty ()
	Is the next highest scoring alignment an empty path with no DP matrices? More...

void	next_empty_alignment (Alignment &alignment)
	Get the next empty path alignment. More...

void	propose_deflection (const IntType score, const int64_t from_node_id, const int64_t row_idx, const int64_t col_idx, const int64_t to_node_id, const matrix_t to_matrix)

IntType	current_traceback_score ()
	Score of the current traceback. More...

const list< int64_t > &	current_empty_prefix ()
	The prefix of the current traceback that consists of only empty nodes. More...

bool	at_next_deflection (int64_t node_id, int64_t row_idx, int64_t col_idx)
	Are these the coordinates of the next deflection? More...

BandedGlobalAligner::matrix_t	deflect_to_matrix ()
	Get the matrix to deflect to and advance to the next deflection. More...

BandedGlobalAligner::matrix_t	deflect_to_matrix (int64_t &to_node_id)
	Get the matrix and the node id to deflect to (for use at a node boundary) More...

Private Member Functions
void	insert_traceback (const vector< Deflection > &traceback_prefix, const IntType score, const int64_t from_node_id, const int64_t row_idx, const int64_t col_idx, const int64_t to_node_id, const matrix_t to_matrix, const list< int64_t > &empty_node_prefix)
	Internal method for propose_deflection. More...

Private Attributes
int64_t	max_multi_alns
	Maximum number of alternate alignments to keep track of (including the optimal alignment) More...

list< tuple< vector< Deflection >, IntType, list< int64_t > > >	alt_tracebacks

list< list< int64_t > >	empty_full_paths
	All of the paths through the graph that take only empty nodes. More...

int32_t	empty_score

const HandleGraph &	graph

list< tuple< vector< Deflection >, IntType, list< int64_t > > >::iterator	curr_traceback
	Pointer to the traceback directions for the alignment we are currently tracing back. More...

vector< Deflection >::iterator	curr_deflxn
	Pointer to the next deviation from the optimal traceback we will take. More...

Detailed Description

template<class IntType>
class vg::BandedGlobalAligner< IntType >::AltTracebackStack

Specialized linked list stack that finds and keeps track of the top-scoring non-optimal alignments. Sub-optimal alignments are represented by the locations where their traceback deviates from the optimal traceback, with other steps of the traceback implicitly following the optimal path. New tracebacks can be discovered while performing any of the tracebacks and added to the stack.

Constructor & Destructor Documentation

◆ AltTracebackStack()

template<class IntType >

vg::BandedGlobalAligner< IntType >::AltTracebackStack::AltTracebackStack	(	const HandleGraph &	graph,
		int64_t	max_multi_alns,
		int32_t	empty_score,
		unordered_set< BAMatrix * > &	source_node_matrices,
		unordered_set< BAMatrix * > &	sink_node_matrices,
		int8_t	gap_open,
		int8_t	gap_extend,
		IntType	min_inf
	)

◆ ~AltTracebackStack()

template<class IntType >

vg::BandedGlobalAligner< IntType >::AltTracebackStack::~AltTracebackStack

Member Function Documentation

◆ at_next_deflection()

template<class IntType >

bool vg::BandedGlobalAligner< IntType >::AltTracebackStack::at_next_deflection	(	int64_t	node_id,
		int64_t	row_idx,
		int64_t	col_idx
	)

inline

Are these the coordinates of the next deflection?

◆ current_empty_prefix()

template<class IntType >

const list< int64_t > & vg::BandedGlobalAligner< IntType >::AltTracebackStack::current_empty_prefix

inline

The prefix of the current traceback that consists of only empty nodes.

◆ current_traceback_score()

template<class IntType >

IntType vg::BandedGlobalAligner< IntType >::AltTracebackStack::current_traceback_score

inline

Score of the current traceback.

◆ deflect_to_matrix() [1/2]

template<class IntType >

BandedGlobalAligner< IntType >::matrix_t vg::BandedGlobalAligner< IntType >::AltTracebackStack::deflect_to_matrix

inline

Get the matrix to deflect to and advance to the next deflection.

◆ deflect_to_matrix() [2/2]

template<class IntType >

BandedGlobalAligner< IntType >::matrix_t vg::BandedGlobalAligner< IntType >::AltTracebackStack::deflect_to_matrix ( int64_t & to_node_id )

inline

Get the matrix and the node id to deflect to (for use at a node boundary)

◆ get_alignment_start()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::AltTracebackStack::get_alignment_start	(	int64_t &	node_id,
		matrix_t &	matrix
	)

inline

Get the start position of the current alignment and advance deflection pointer to the first deflection.

◆ has_next()

template<class IntType >

bool vg::BandedGlobalAligner< IntType >::AltTracebackStack::has_next

inline

Are there any more alternate alignments in the stack?

◆ insert_traceback()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::AltTracebackStack::insert_traceback	(	const vector< Deflection > &	traceback_prefix,
		const IntType	score,
		const int64_t	from_node_id,
		const int64_t	row_idx,
		const int64_t	col_idx,
		const int64_t	to_node_id,
		const matrix_t	to_matrix,
		const list< int64_t > &	empty_node_prefix
	)

inlineprivate

Internal method for propose_deflection.

◆ next_empty_alignment()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::AltTracebackStack::next_empty_alignment ( Alignment & alignment )

inline

Get the next empty path alignment.

◆ next_is_empty()

template<class IntType >

bool vg::BandedGlobalAligner< IntType >::AltTracebackStack::next_is_empty

inline

Is the next highest scoring alignment an empty path with no DP matrices?

◆ next_traceback_alignment()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::AltTracebackStack::next_traceback_alignment

inline

Advance to the next alternate trac.

◆ propose_deflection()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::AltTracebackStack::propose_deflection	(	const IntType	score,
		const int64_t	from_node_id,
		const int64_t	row_idx,
		const int64_t	col_idx,
		const int64_t	to_node_id,
		const matrix_t	to_matrix
	)

inline

Check if a deflection from the current traceback is better than any alignments currently in the stack and if so insert it in the correct position

Member Data Documentation

◆ alt_tracebacks

template<class IntType >

list<tuple<vector<Deflection>, IntType, list<int64_t> > > vg::BandedGlobalAligner< IntType >::AltTracebackStack::alt_tracebacks

private

List of tuples that contain the scores of alternate alignments, the places where their traceback deviates from the optimum (Deflections), and all empty nodes that occur at the suffix of the traceback (if any). Maintains an invariant where stack is sorted in descending score order.

◆ curr_deflxn

template<class IntType >

vector<Deflection>::iterator vg::BandedGlobalAligner< IntType >::AltTracebackStack::curr_deflxn

private

Pointer to the next deviation from the optimal traceback we will take.

◆ curr_traceback

template<class IntType >

list<tuple<vector<Deflection>, IntType, list<int64_t> > >::iterator vg::BandedGlobalAligner< IntType >::AltTracebackStack::curr_traceback

private

Pointer to the traceback directions for the alignment we are currently tracing back.

◆ empty_full_paths

template<class IntType >

list<list<int64_t> > vg::BandedGlobalAligner< IntType >::AltTracebackStack::empty_full_paths

private

All of the paths through the graph that take only empty nodes.

◆ empty_score

template<class IntType >

int32_t vg::BandedGlobalAligner< IntType >::AltTracebackStack::empty_score

private

◆ graph

template<class IntType >

const HandleGraph& vg::BandedGlobalAligner< IntType >::AltTracebackStack::graph

private

◆ max_multi_alns

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::AltTracebackStack::max_multi_alns

private

Maximum number of alternate alignments to keep track of (including the optimal alignment)

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

src/banded_global_aligner.hpp
src/banded_global_aligner.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

template<class IntType> class vg::BandedGlobalAligner< IntType >::AltTracebackStack

Constructor & Destructor Documentation

◆ AltTracebackStack()

◆ ~AltTracebackStack()

Member Function Documentation

◆ at_next_deflection()

◆ current_empty_prefix()

◆ current_traceback_score()

◆ deflect_to_matrix() [1/2]

◆ deflect_to_matrix() [2/2]

◆ get_alignment_start()

◆ has_next()

◆ insert_traceback()

◆ next_empty_alignment()

◆ next_is_empty()

◆ next_traceback_alignment()

◆ propose_deflection()

Member Data Documentation

◆ alt_tracebacks

◆ curr_deflxn

◆ curr_traceback

◆ empty_full_paths

◆ empty_score

◆ graph

◆ max_multi_alns

template<class IntType>
class vg::BandedGlobalAligner< IntType >::AltTracebackStack