vg::QualAdjXdropAligner Class Reference

#include <dozeu_interface.hpp>

Inheritance diagram for vg::QualAdjXdropAligner:

Public Member Functions
	QualAdjXdropAligner (const int8_t *_score_matrix, const int8_t *_qual_adj_score_matrix, int8_t _gap_open, int8_t _gap_extension)
	Main constructor. Expects a 4 x 4 score matrix and a 4 x 4 x 64 quality adjusted matrix.
	QualAdjXdropAligner ()=default
	~QualAdjXdropAligner (void)
	QualAdjXdropAligner (const QualAdjXdropAligner &other)
	Copy constructor.
QualAdjXdropAligner &	operator= (const QualAdjXdropAligner &other)
	Copy assignment.
	QualAdjXdropAligner (QualAdjXdropAligner &&other)
	Move constructor.
QualAdjXdropAligner &	operator= (QualAdjXdropAligner &&other)
	Move assignment.
Public Member Functions inherited from vg::DozeuInterface
virtual	~DozeuInterface ()=default
void	align (Alignment &alignment, const HandleGraph &graph, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)
void	align (Alignment &alignment, const HandleGraph &graph, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)
void	align_pinned (Alignment &alignment, const HandleGraph &g, bool pin_left, int8_t full_length_bonus, uint16_t max_gap_length=default_xdrop_max_gap_length)

Private Member Functions
dz_query_s *	pack_query_forward (const char *seq, const uint8_t *qual, int8_t full_length_bonus, size_t len)
dz_query_s *	pack_query_reverse (const char *seq, const uint8_t *qual, int8_t full_length_bonus, size_t len)
const dz_forefront_s *	scan (const dz_query_s *query, const dz_forefront_s **forefronts, size_t n_forefronts, const char *ref, int32_t rlen, uint32_t rid, uint16_t xt)
const dz_forefront_s *	extend (const dz_query_s *query, const dz_forefront_s **forefronts, size_t n_forefronts, const char *ref, int32_t rlen, uint32_t rid, uint16_t xt)
dz_alignment_s *	trace (const dz_forefront_s *forefront)
void	flush ()

Additional Inherited Members
Static Public Attributes inherited from vg::DozeuInterface
static constexpr size_t	THREAD_MAX_RETAINED_BYTES = 2ULL * 1024 * 1024 * 1024
Protected Member Functions inherited from vg::DozeuInterface
graph_pos_s	calculate_seed_position (const OrderedGraph &graph, const vector< MaximalExactMatch > &mems, size_t query_length, bool direction) const
graph_pos_s	calculate_max_position (const OrderedGraph &graph, const graph_pos_s &seed_pos, size_t max_node_index, bool direction, const vector< const dz_forefront_s * > &forefronts)
pair< graph_pos_s, bool >	scan_seed_position (const OrderedGraph &graph, const Alignment &alignment, bool direction, vector< const dz_forefront_s * > &forefronts, int8_t full_length_bonus, uint16_t max_gap_length)
size_t	push_edit (Mapping *mapping, uint8_t op, const char *alt, size_t len) const
size_t	do_poa (const OrderedGraph &graph, const dz_query_s *packed_query, const vector< graph_pos_s > &seed_positions, bool right_to_left, vector< const dz_forefront_s * > &forefronts, uint16_t)
void	calculate_and_save_alignment (Alignment &alignment, const OrderedGraph &graph, const vector< graph_pos_s > &head_positions, size_t tail_node_index, bool left_to_right, const vector< const dz_forefront_s * > &forefronts)
void	align_downward (Alignment &alignment, const OrderedGraph &graph, const vector< graph_pos_s > &head_positions, bool left_to_right, vector< const dz_forefront_s * > &forefronts, int8_t full_length_bonus, uint16_t max_gap_length)
Protected Attributes inherited from vg::DozeuInterface
dz_s *	dz = nullptr
	The core dozeu class, which does the alignments.

Constructor & Destructor Documentation

QualAdjXdropAligner() [1/4]

QualAdjXdropAligner::QualAdjXdropAligner	(	const int8_t *	_score_matrix,
		const int8_t *	_qual_adj_score_matrix,
		int8_t	_gap_open,
		int8_t	_gap_extension )

Main constructor. Expects a 4 x 4 score matrix and a 4 x 4 x 64 quality adjusted matrix.

QualAdjXdropAligner() [2/4]

vg::QualAdjXdropAligner::QualAdjXdropAligner ( )

default

~QualAdjXdropAligner()

QualAdjXdropAligner::~QualAdjXdropAligner

(

void

)

QualAdjXdropAligner() [3/4]

QualAdjXdropAligner::QualAdjXdropAligner

(

const QualAdjXdropAligner &

other

)

Copy constructor.

QualAdjXdropAligner() [4/4]

QualAdjXdropAligner::QualAdjXdropAligner

(

QualAdjXdropAligner &&

other

)

Move constructor.

Member Function Documentation

extend()

const dz_forefront_s * QualAdjXdropAligner::extend ( const dz_query_s * query, const dz_forefront_s ** forefronts, size_t n_forefronts, const char * ref, int32_t rlen, uint32_t rid, uint16_t xt )

privatevirtual

Implements vg::DozeuInterface.

flush()

void QualAdjXdropAligner::flush ( )

privatevirtual

Implements vg::DozeuInterface.

operator=() [1/2]

QualAdjXdropAligner & QualAdjXdropAligner::operator=

(

const QualAdjXdropAligner &

other

)

Copy assignment.

operator=() [2/2]

QualAdjXdropAligner & QualAdjXdropAligner::operator=

(

QualAdjXdropAligner &&

other

)

Move assignment.

pack_query_forward()

dz_query_s * QualAdjXdropAligner::pack_query_forward ( const char * seq, const uint8_t * qual, int8_t full_length_bonus, size_t len )

privatevirtual

Implements vg::DozeuInterface.

pack_query_reverse()

dz_query_s * QualAdjXdropAligner::pack_query_reverse ( const char * seq, const uint8_t * qual, int8_t full_length_bonus, size_t len )

privatevirtual

Implements vg::DozeuInterface.

scan()

const dz_forefront_s * QualAdjXdropAligner::scan ( const dz_query_s * query, const dz_forefront_s ** forefronts, size_t n_forefronts, const char * ref, int32_t rlen, uint32_t rid, uint16_t xt )

privatevirtual

Implements vg::DozeuInterface.

trace()

dz_alignment_s * QualAdjXdropAligner::trace ( const dz_forefront_s * forefront )

privatevirtual

Implements vg::DozeuInterface.

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

• src/dozeu_interface.hpp
• src/qual_adj_xdrop_aligner.cpp