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

#include <banded_global_aligner.hpp>

Public Member Functions
	BAMatrix (Alignment &alignment, handle_t node, int64_t top_diag, int64_t bottom_diag, const vector< BAMatrix * > &seeds, int64_t cumulative_seq_len)
	~BAMatrix ()
void	fill_matrix (const HandleGraph &graph, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf)
	Use DP to fill the band with alignment scores. More...
void	traceback (const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, matrix_t start_mat, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf)
	Traceback through the band after using DP to fill it. More...
void	print_full_matrices (const HandleGraph &graph)
	Debugging function. More...
void	print_rectangularized_bands (const HandleGraph &graph)
	Debugging function. More...

Private Member Functions
void	traceback_internal (const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t start_row, int64_t start_col, matrix_t start_mat, bool in_lead_gap, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf)
void	print_matrix (const HandleGraph &graph, matrix_t which_mat)
	Debugging function. More...
void	print_band (const HandleGraph &graph, matrix_t which_mat)
	Debugging function. More...

Private Attributes
int64_t	top_diag
	The diagonals in the DP matrix that the band passes through with the bottom index inclusive. More...
int64_t	bottom_diag
handle_t	node
Alignment &	alignment
int64_t	cumulative_seq_len
	Length of shortest sequence leading to matrix from a source node. More...
vector< BAMatrix * >	seeds
	Matrices for nodes with edges into this node. More...
IntType *	match
	DP matrix. More...
IntType *	insert_col
	DP matrix. More...
IntType *	insert_row
	DP matrix. More...

Friends
class	BABuilder
class	AltTracebackStack

Detailed Description

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

Represents the band from the DP matrix for one node in the graph

Constructor & Destructor Documentation

BAMatrix()

template<class IntType >

vg::BandedGlobalAligner< IntType >::BAMatrix::BAMatrix	(	Alignment &	alignment,
		handle_t	node,
		int64_t	top_diag,
		int64_t	bottom_diag,
		const vector< BAMatrix * > &	seeds,
		int64_t	cumulative_seq_len
	)

~BAMatrix()

template<class IntType >

vg::BandedGlobalAligner< IntType >::BAMatrix::~BAMatrix

(

)

Member Function Documentation

fill_matrix()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::fill_matrix	(	const HandleGraph &	graph,
		int8_t *	score_mat,
		int8_t *	nt_table,
		int8_t	gap_open,
		int8_t	gap_extend,
		bool	qual_adjusted,
		IntType	min_inf
	)

Use DP to fill the band with alignment scores.

print_band()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::print_band ( const HandleGraph &  graph, matrix_t  which_mat  )

private

Debugging function.

print_full_matrices()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::print_full_matrices

(

const HandleGraph &

graph

)

Debugging function.

print_matrix()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::print_matrix ( const HandleGraph &  graph, matrix_t  which_mat  )

private

Debugging function.

print_rectangularized_bands()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::print_rectangularized_bands

(

const HandleGraph &

graph

)

Debugging function.

traceback()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::traceback	(	const HandleGraph &	graph,
		BABuilder &	builder,
		AltTracebackStack &	traceback_stack,
		matrix_t	start_mat,
		int8_t *	score_mat,
		int8_t *	nt_table,
		int8_t	gap_open,
		int8_t	gap_extend,
		bool	qual_adjusted,
		IntType	min_inf
	)

Traceback through the band after using DP to fill it.

traceback_internal()

template<class IntType >

void vg::BandedGlobalAligner< IntType >::BAMatrix::traceback_internal ( const HandleGraph &  graph, BABuilder &  builder, AltTracebackStack &  traceback_stack, int64_t  start_row, int64_t  start_col, matrix_t  start_mat, bool  in_lead_gap, int8_t *  score_mat, int8_t *  nt_table, int8_t  gap_open, int8_t  gap_extend, bool  qual_adjusted, IntType  min_inf  )

private

Friends And Related Function Documentation

AltTracebackStack

template<class IntType >

friend class AltTracebackStack

friend

BABuilder

template<class IntType >

friend class BABuilder

friend

Member Data Documentation

alignment

template<class IntType >

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

private

bottom_diag

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::BAMatrix::bottom_diag

private

cumulative_seq_len

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::BAMatrix::cumulative_seq_len

private

Length of shortest sequence leading to matrix from a source node.

insert_col

template<class IntType >

IntType* vg::BandedGlobalAligner< IntType >::BAMatrix::insert_col

private

DP matrix.

insert_row

template<class IntType >

IntType* vg::BandedGlobalAligner< IntType >::BAMatrix::insert_row

private

DP matrix.

match

template<class IntType >

IntType* vg::BandedGlobalAligner< IntType >::BAMatrix::match

private

DP matrix.

node

template<class IntType >

handle_t vg::BandedGlobalAligner< IntType >::BAMatrix::node

private

seeds

template<class IntType >

vector<BAMatrix*> vg::BandedGlobalAligner< IntType >::BAMatrix::seeds

private

Matrices for nodes with edges into this node.

top_diag

template<class IntType >

int64_t vg::BandedGlobalAligner< IntType >::BAMatrix::top_diag

private

The diagonals in the DP matrix that the band passes through with the bottom index inclusive.

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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