vg::DeletionAligner Class Reference

#include <deletion_aligner.hpp>

Public Member Functions
	DeletionAligner (int8_t gap_open, int8_t gap_extension)
	DeletionAligner ()=default
	~DeletionAligner ()=default
void	align (Alignment &aln, const HandleGraph &graph) const
void	align_multi (Alignment &aln, vector< Alignment > &alt_alns, const HandleGraph &graph, int32_t max_alt_alns) const

Private Member Functions
vector< vector< handle_t > >	run_dp (const HandleGraph &graph, int32_t max_tracebacks) const
pair< vector< size_t >, vector< pair< size_t, size_t > > >	min_dists (const vector< handle_t > &order, const unordered_map< handle_t, size_t > &index_of, const HandleGraph &graph) const
vector< vector< handle_t > >	traceback (const vector< handle_t > &order, const unordered_map< handle_t, size_t > &index_of, const HandleGraph &graph, const vector< size_t > &dists, const vector< pair< size_t, size_t >> &sinks, size_t max_tracebacks) const
void	trace_to_alignment (Alignment &aln, const vector< handle_t > &trace, const HandleGraph &graph) const

Private Attributes
int32_t	gap_open
int32_t	gap_extension

Constructor & Destructor Documentation

DeletionAligner() [1/2]

vg::DeletionAligner::DeletionAligner	(	int8_t	gap_open,
		int8_t	gap_extension
	)

DeletionAligner() [2/2]

vg::DeletionAligner::DeletionAligner ( )

default

~DeletionAligner()

vg::DeletionAligner::~DeletionAligner ( )

default

Member Function Documentation

align()

void vg::DeletionAligner::align	(	Alignment &	aln,
		const HandleGraph &	graph
	)		const

align_multi()

void vg::DeletionAligner::align_multi	(	Alignment &	aln,
		vector< Alignment > &	alt_alns,
		const HandleGraph &	graph,
		int32_t	max_alt_alns
	)		const

min_dists()

pair< vector< size_t >, vector< pair< size_t, size_t > > > vg::DeletionAligner::min_dists ( const vector< handle_t > &  order, const unordered_map< handle_t, size_t > &  index_of, const HandleGraph &  graph  ) const

private

run_dp()

vector< vector< handle_t > > vg::DeletionAligner::run_dp ( const HandleGraph &  graph, int32_t  max_tracebacks  ) const

private

trace_to_alignment()

void vg::DeletionAligner::trace_to_alignment ( Alignment &  aln, const vector< handle_t > &  trace, const HandleGraph &  graph  ) const

private

traceback()

vector< vector< handle_t > > vg::DeletionAligner::traceback ( const vector< handle_t > &  order, const unordered_map< handle_t, size_t > &  index_of, const HandleGraph &  graph, const vector< size_t > &  dists, const vector< pair< size_t, size_t >> &  sinks, size_t  max_tracebacks  ) const

private

Member Data Documentation

gap_extension

int32_t vg::DeletionAligner::gap_extension

private

gap_open

int32_t vg::DeletionAligner::gap_open

private

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

• src/deletion_aligner.hpp
• src/deletion_aligner.cpp