vg::BandedGlobalAligner< IntType >::BABuilder Class Reference

#include <banded_global_aligner.hpp>

Public Member Functions
	BABuilder (Alignment &alignment)
	~BABuilder ()
void	update_state (const HandleGraph &graph, matrix_t matrix, const handle_t &node, int64_t read_idx, int64_t node_idx, bool empty_node_seq=false)
	Add next step in traceback. More...
void	finalize_alignment (const list< int64_t > &empty_prefix)
	Call after concluding traceback to finish adding edits to alignment. More...

Private Member Functions
void	finish_current_edit ()
void	finish_current_node ()

Private Attributes
Alignment &	alignment
list< Mapping >	node_mappings
list< Edit >	mapping_edits
matrix_t	matrix_state
bool	matching = false
id_t	current_node_id = 0
string	current_node_sequence = ""
int64_t	edit_length = 0
int64_t	edit_read_end_idx = 0

Detailed Description

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

Translates a traceback path into a Path object and stores it in an Alignment object

Constructor & Destructor Documentation

BABuilder()

template<class IntType >

vg::BandedGlobalAligner< IntType >::BABuilder::BABuilder

(

Alignment &

alignment

)

~BABuilder()

template<class IntType >

vg::BandedGlobalAligner< IntType >::BABuilder::~BABuilder

Member Function Documentation

finalize_alignment()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BABuilder::finalize_alignment

(

const list< int64_t > &

empty_prefix

)

Call after concluding traceback to finish adding edits to alignment.

finish_current_edit()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BABuilder::finish_current_edit

private

finish_current_node()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BABuilder::finish_current_node

private

update_state()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BABuilder::update_state	(	const HandleGraph &	graph,
		matrix_t	matrix,
		const handle_t &	node,
		int64_t	read_idx,
		int64_t	node_idx,
		bool	empty_node_seq = false
	)

Add next step in traceback.

Member Data Documentation

alignment

template<class IntType >

Alignment& vg::BandedGlobalAligner< IntType >::BABuilder::alignment

private

current_node_id

template<class IntType >

id_t vg::BandedGlobalAligner< IntType >::BABuilder::current_node_id = 0

private

current_node_sequence

template<class IntType >

string vg::BandedGlobalAligner< IntType >::BABuilder::current_node_sequence = ""

private

edit_length

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::BABuilder::edit_length = 0

private

edit_read_end_idx

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::BABuilder::edit_read_end_idx = 0

private

mapping_edits

template<class IntType >

list<Edit> vg::BandedGlobalAligner< IntType >::BABuilder::mapping_edits

private

matching

template<class IntType >

bool vg::BandedGlobalAligner< IntType >::BABuilder::matching = false

private

matrix_state

template<class IntType >

matrix_t vg::BandedGlobalAligner< IntType >::BABuilder::matrix_state

private

node_mappings

template<class IntType >

list<Mapping> vg::BandedGlobalAligner< IntType >::BABuilder::node_mappings

private

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

• src/banded_global_aligner.hpp
• src/banded_global_aligner.cpp