This is the complete list of members for vg::QualAdjAligner, including all inherited members.

align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) const override	vg::QualAdjAligner	virtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, uint64_t max_cells=std::numeric_limits< uint64_t >::max()) const override	vg::QualAdjAligner	virtual
align_global_banded_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true, uint64_t max_cells=std::numeric_limits< uint64_t >::max()) const override	vg::QualAdjAligner	virtual
align_internal(Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) const	vg::QualAdjAligner	protected
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) const override	vg::QualAdjAligner	virtual
align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const override	vg::QualAdjAligner	virtual
align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const override	vg::QualAdjAligner	virtual
align_xdrop(Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const override	vg::QualAdjAligner	virtual
create_gssw_graph(const HandleGraph &g) const	vg::GSSWAligner	protected
deletion_aligner	vg::GSSWAligner	protected
graph_cigar(gssw_graph_mapping *gm) const	vg::GSSWAligner	protected
gssw_mapping_to_alignment(gssw_graph graph, gssw_graph_mapping gm, Alignment &alignment, bool pinned, bool pin_left) const	vg::GSSWAligner	protected
GSSWAligner(std::unique_ptr< MatrixAlignmentScorer > owned_scorer)	vg::GSSWAligner	protected
GSSWAligner(GSSWAligner &&)=default	vg::GSSWAligner
GSSWAligner(const GSSWAligner &)=delete	vg::GSSWAligner
identify_pinning_points(const HandleGraph &graph) const	vg::GSSWAligner	protected
mapq_calc	vg::GSSWAligner
operator=(QualAdjAligner &&)=default	vg::QualAdjAligner
vg::GSSWAligner::operator=(GSSWAligner &&)=default	vg::GSSWAligner
vg::GSSWAligner::operator=(const GSSWAligner &)=delete	vg::GSSWAligner
QualAdjAligner(const int8_t *score_matrix=default_score_matrix, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus, double gc_content=default_gc_content)	vg::QualAdjAligner
QualAdjAligner(QualAdjAligner &&)=default	vg::QualAdjAligner
scorer	vg::GSSWAligner
unreverse_graph(gssw_graph *graph) const	vg::GSSWAligner	protected
unreverse_graph_mapping(gssw_graph_mapping *gm) const	vg::GSSWAligner	protected
xdrops	vg::QualAdjAligner	protected
~GSSWAligner()	vg::GSSWAligner	protected