vg
tools for working with variation graphs
Loading...
Searching...
No Matches
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

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