diff --git a/classvg_1_1Aligner-members.html b/classvg_1_1Aligner-members.html index b24f6636657..cc2f982912a 100644 --- a/classvg_1_1Aligner-members.html +++ b/classvg_1_1Aligner-members.html @@ -75,8 +75,8 @@ - - + + diff --git a/classvg_1_1Aligner.html b/classvg_1_1Aligner.html index 2d3a4c68752..a36730fb3e4 100644 --- a/classvg_1_1Aligner.html +++ b/classvg_1_1Aligner.html @@ -102,10 +102,10 @@ - - - - + + + + @@ -404,8 +404,8 @@

-

◆ align_global_banded()

+ +

◆ align_global_banded()

@@ -435,7 +435,13 @@

- + + + + + + + @@ -451,12 +457,12 @@

store optimal global alignment against a graph within a specified band in the Alignment object permissive banding auto detects the width of band needed so that paths can travel through every node in the graph

-

Implements vg::GSSWAligner.

+

Implements vg::GSSWAligner.

- -

◆ align_global_banded_multi()

+ +

◆ align_global_banded_multi()

@@ -498,7 +504,13 @@

- + + + + + + + @@ -514,7 +526,7 @@

store top scoring global alignments in the vector in descending score order up to a maximum number of alternate alignments (including the optimal alignment). if there are fewer than the maximum number of alignments in the return value, then the vector contains all possible alignments. the optimal alignment will be stored in both the vector and the original alignment object

-

Implements vg::GSSWAligner.

+

Implements vg::GSSWAligner.

diff --git a/classvg_1_1BandedGlobalAligner-members.html b/classvg_1_1BandedGlobalAligner-members.html index 7eb4616fb4f..b02b378c521 100644 --- a/classvg_1_1BandedGlobalAligner-members.html +++ b/classvg_1_1BandedGlobalAligner-members.html @@ -78,9 +78,9 @@

- - - + + + diff --git a/classvg_1_1BandedGlobalAligner.html b/classvg_1_1BandedGlobalAligner.html index 7838477dff6..5f431950966 100644 --- a/classvg_1_1BandedGlobalAligner.html +++ b/classvg_1_1BandedGlobalAligner.html @@ -91,10 +91,10 @@
align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) constvg::Alignervirtual
align(Alignment &alignment, const HandleGraph &g, const std::vector< handle_t > &topological_order) constvg::Aligner
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) constvg::Alignervirtual
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) constvg::Alignervirtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) constvg::Alignervirtual
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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) constvg::Alignervirtual
align_internal(Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) constvg::Alignerprivate
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) constvg::Alignervirtual
align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) constvg::Alignervirtual
 
void align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const
 
void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const
 
void 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) const
 
void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const
 
void 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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const
 
void 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
 xdrop aligner More...
 
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
alignmentvg::BandedGlobalAligner< IntType >private
alt_alignmentsvg::BandedGlobalAligner< IntType >private
banded_matricesvg::BandedGlobalAligner< IntType >private
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)vg::BandedGlobalAligner< IntType >
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)vg::BandedGlobalAligner< IntType >
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)vg::BandedGlobalAligner< IntType >private
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::BandedGlobalAligner< IntType >
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::BandedGlobalAligner< IntType >
BandedGlobalAligner(Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::BandedGlobalAligner< IntType >private
find_banded_paths(bool permissive_banding, int64_t band_padding, vector< bool > &node_masked, vector< pair< int64_t, int64_t >> &band_ends)vg::BandedGlobalAligner< IntType >private
graphvg::BandedGlobalAligner< IntType >private
InsertCol enum valuevg::BandedGlobalAligner< IntType >private
- - - - + + + + @@ -111,9 +111,9 @@

Public Member Functions

 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)
 
 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)
 
 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, vector< Alignment > &alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
 ~BandedGlobalAligner ()
 
void align (int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend)
- - - + + + @@ -165,7 +165,7 @@

The outward-facing interface for banded global graph alignment. It computes optimal alignment of a DNA sequence to a DAG with POA. The alignment will start at any source node in the graph and end at any sink node. It is also restricted to falling within a certain diagonal band from the start node. Any signed integer type can be used for the dynamic programming matrices, but there are no checks for overflow.

THIS IS A COMPONENT OF THE ALIGNER CLASS.

-

Use Aligner::align_global_banded() instead.

+

Use Aligner::align_global_banded() instead.

Member Enumeration Documentation

◆ matrix_t

@@ -199,8 +199,8 @@

Constructor & Destructor Documentation

- -

◆ BandedGlobalAligner() [1/3]

+ +

◆ BandedGlobalAligner() [1/3]

@@ -235,7 +235,13 @@

- + + + + + + + @@ -249,8 +255,8 @@

-

◆ BandedGlobalAligner() [2/3]

+ +

◆ BandedGlobalAligner() [2/3]

@@ -297,7 +303,13 @@

- + + + + + + + @@ -327,8 +339,8 @@

-

◆ BandedGlobalAligner() [3/3]

+ +

◆ BandedGlobalAligner() [3/3]

@@ -378,7 +390,13 @@

- + + + + + + + diff --git a/classvg_1_1BandedGlobalAligner_1_1BAMatrix-members.html b/classvg_1_1BandedGlobalAligner_1_1BAMatrix-members.html index 834bfb3a7f1..67e4fca3a56 100644 --- a/classvg_1_1BandedGlobalAligner_1_1BAMatrix-members.html +++ b/classvg_1_1BandedGlobalAligner_1_1BAMatrix-members.html @@ -76,7 +76,7 @@ - + @@ -84,17 +84,18 @@ - - - - - - - - - - - + + + + + + + + + + + +

Private Member Functions

 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false)
 Internal constructor that the public constructors funnel into. More...
 
 BandedGlobalAligner (Alignment &alignment, const HandleGraph &g, vector< Alignment > *alt_alignments, int64_t max_multi_alns, int64_t band_padding, bool permissive_banding=false, bool adjust_for_base_quality=false, const unordered_map< handle_t, bool > *left_align_strand=nullptr)
 Internal constructor that the public constructors funnel into. More...
 
void traceback (int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, IntType min_inf)
 Traceback through dynamic programming matrices to compute alignment. More...
 
bool adjust_for_base_quality = false adjust_for_base_quality = false,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool adjust_for_base_quality = false adjust_for_base_quality = false,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool adjust_for_base_quality = false adjust_for_base_quality = false,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
alignmentvg::BandedGlobalAligner< IntType >::BAMatrixprivate
AltTracebackStack classvg::BandedGlobalAligner< IntType >::BAMatrixfriend
BABuilder classvg::BandedGlobalAligner< IntType >::BAMatrixfriend
BAMatrix(Alignment &alignment, handle_t node, int64_t top_diag, int64_t bottom_diag, const vector< BAMatrix * > &seeds, int64_t cumulative_seq_len)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, bool left_alignment_strand)vg::BandedGlobalAligner< IntType >::BAMatrix
BandedGlobalAligner classvg::BandedGlobalAligner< IntType >::BAMatrixfriend
bottom_diagvg::BandedGlobalAligner< IntType >::BAMatrixprivate
cumulative_seq_lenvg::BandedGlobalAligner< IntType >::BAMatrixprivate
init_traceback_indexes(const HandleGraph &graph, int64_t &i, int64_t &j)vg::BandedGlobalAligner< IntType >::BAMatrix
insert_colvg::BandedGlobalAligner< IntType >::BAMatrixprivate
insert_rowvg::BandedGlobalAligner< IntType >::BAMatrixprivate
matchvg::BandedGlobalAligner< IntType >::BAMatrixprivate
nodevg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_band(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_full_matrices(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
print_matrix(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_rectangularized_bands(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
seedsvg::BandedGlobalAligner< IntType >::BAMatrixprivate
top_diagvg::BandedGlobalAligner< IntType >::BAMatrixprivate
traceback(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf)vg::BandedGlobalAligner< IntType >::BAMatrix
traceback_over_edge(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, int64_t &node_id, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf)vg::BandedGlobalAligner< IntType >::BAMatrix
~BAMatrix()vg::BandedGlobalAligner< IntType >::BAMatrix
left_alignment_strandvg::BandedGlobalAligner< IntType >::BAMatrixprivate
matchvg::BandedGlobalAligner< IntType >::BAMatrixprivate
nodevg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_band(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_full_matrices(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
print_matrix(const HandleGraph &graph, matrix_t which_mat)vg::BandedGlobalAligner< IntType >::BAMatrixprivate
print_rectangularized_bands(const HandleGraph &graph)vg::BandedGlobalAligner< IntType >::BAMatrix
seedsvg::BandedGlobalAligner< IntType >::BAMatrixprivate
top_diagvg::BandedGlobalAligner< IntType >::BAMatrixprivate
traceback(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf)vg::BandedGlobalAligner< IntType >::BAMatrix
traceback_over_edge(const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t &i, int64_t &j, matrix_t &mat, bool &in_lead_gap, int64_t &node_id, const int8_t *score_mat, const int8_t *nt_table, const int8_t gap_open, const int8_t gap_extend, const bool qual_adjusted, IntType const min_inf)vg::BandedGlobalAligner< IntType >::BAMatrix
~BAMatrix()vg::BandedGlobalAligner< IntType >::BAMatrix
diff --git a/classvg_1_1BandedGlobalAligner_1_1BAMatrix.html b/classvg_1_1BandedGlobalAligner_1_1BAMatrix.html index 7c7c9ad0e21..afa08d2b383 100644 --- a/classvg_1_1BandedGlobalAligner_1_1BAMatrix.html +++ b/classvg_1_1BandedGlobalAligner_1_1BAMatrix.html @@ -81,8 +81,8 @@ - - + + @@ -119,6 +119,8 @@ + + @@ -152,8 +154,8 @@

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

Constructor & Destructor Documentation

- -

◆ BAMatrix()

+ +

◆ BAMatrix()

@@ -194,7 +196,13 @@

- + + + + + + + @@ -841,6 +849,30 @@

+

◆ left_alignment_strand

+ +
+
+
+template<class IntType >
+

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 (Alignment &alignment, handle_t node, int64_t top_diag, int64_t bottom_diag, const vector< BAMatrix * > &seeds, int64_t cumulative_seq_len, bool left_alignment_strand)
 
 ~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)
 
handle_t node
 
bool left_alignment_strand
 
Alignment & alignment
 
int64_t cumulative_seq_len
int64_t cumulative_seq_len cumulative_seq_len,
bool left_alignment_strand 
+ + + + +
+ + + + +
bool vg::BandedGlobalAligner< IntType >::BAMatrix::left_alignment_strand
+ 		+private
+
+
diff --git a/classvg_1_1GSSWAligner-members.html b/classvg_1_1GSSWAligner-members.html index 392a53976dd..7555647e6ba 100644 --- a/classvg_1_1GSSWAligner-members.html +++ b/classvg_1_1GSSWAligner-members.html @@ -74,8 +74,8 @@

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

- - + + diff --git a/classvg_1_1GSSWAligner.html b/classvg_1_1GSSWAligner.html index ec06f7d7b6e..70bb2a3537c 100644 --- a/classvg_1_1GSSWAligner.html +++ b/classvg_1_1GSSWAligner.html @@ -100,10 +100,10 @@ - - - - + + + + @@ -339,8 +339,8 @@

Member Function Documentation

- -

◆ align_global_banded()

+ +

◆ align_global_banded()

@@ -370,7 +370,13 @@

- + + + + + + + @@ -386,12 +392,12 @@

store optimal global alignment against a graph within a specified band in the Alignment object permissive banding auto detects the width of band needed so that paths can travel through every node in the graph

-

Implemented in vg::QualAdjAligner, and vg::Aligner.

+

Implemented in vg::QualAdjAligner, and vg::Aligner.

- -

◆ align_global_banded_multi()

+ +

◆ align_global_banded_multi()

@@ -433,7 +439,13 @@

- + + + + + + + @@ -449,7 +461,7 @@

store top scoring global alignments in the vector in descending score order up to a maximum number of alternate alignments (including the optimal alignment). if there are fewer than the maximum number of alignments in the return value, then the vector contains all possible alignments. the optimal alignment will be stored in both the vector and the original alignment object

-

Implemented in vg::QualAdjAligner, and vg::Aligner.

+

Implemented in vg::QualAdjAligner, and vg::Aligner.

diff --git a/classvg_1_1MultipathAlignmentGraph-members.html b/classvg_1_1MultipathAlignmentGraph-members.html index cb7fd8f07d6..7a28e2002fd 100644 --- a/classvg_1_1MultipathAlignmentGraph-members.html +++ b/classvg_1_1MultipathAlignmentGraph-members.html @@ -75,8 +75,8 @@

align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) const =0vg::BaseAlignerpure virtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const =0vg::GSSWAlignerpure 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) const =0vg::GSSWAlignerpure virtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const =0vg::GSSWAlignerpure 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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const =0vg::GSSWAlignerpure virtual
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 =0vg::GSSWAlignerpure virtual
align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const =0vg::GSSWAlignerpure 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 =0vg::GSSWAlignerpure virtual
 
virtual void align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const =0
 
virtual void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const =0
 
virtual void 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) const =0
 
virtual void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const =0
 
virtual void 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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const =0
 
virtual void 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 =0
 xdrop aligner More...
 
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
- - + + diff --git a/classvg_1_1MultipathAlignmentGraph.html b/classvg_1_1MultipathAlignmentGraph.html index bec75172202..df532997cc8 100644 --- a/classvg_1_1MultipathAlignmentGraph.html +++ b/classvg_1_1MultipathAlignmentGraph.html @@ -128,10 +128,10 @@ - - - - + + + + @@ -920,8 +920,8 @@

-

◆ align() [1/2]

+ +

◆ align() [1/2]

@@ -1020,7 +1020,13 @@

- + + + + + + + @@ -1034,8 +1040,8 @@

-

◆ align() [2/2]

+ +

◆ align() [2/2]

@@ -1134,7 +1140,13 @@

- + + + + + + + diff --git a/classvg_1_1QualAdjAligner-members.html b/classvg_1_1QualAdjAligner-members.html index e0baa0cf5ba..b26b82b8651 100644 --- a/classvg_1_1QualAdjAligner-members.html +++ b/classvg_1_1QualAdjAligner-members.html @@ -74,8 +74,8 @@

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

add_decomposed_tail_alignments(const Alignment &alignment, const HandleGraph &align_graph, multipath_alignment_t &multipath_aln_out, unordered_set< size_t > &prohibited_merges, vector< pair< path_t, int32_t >> &shared_tail_alns, vector< vector< pair< path_t, int32_t >>> &unshared_tail_alns, size_t attachment_idx, bool to_left, size_t unmergeable_len, const GSSWAligner *aligner, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr)vg::MultipathAlignmentGraphprotected
add_reachability_edges(const HandleGraph &vg, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)vg::MultipathAlignmentGraph
align_tails(const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, size_t min_paths, unordered_set< size_t > *sources=nullptr)vg::MultipathAlignmentGraphprotected
clear_reachability_edges()vg::MultipathAlignmentGraph
collapse_order_length_runs(const HandleGraph &graph, gcsa::GCSA *gcsa, vector< size_t > &path_node_provenance)vg::MultipathAlignmentGraphprotected
void add_reachability_edges (const HandleGraph &vg, const function< pair< id_t, bool >(id_t)> &project, const unordered_multimap< id_t, pair< id_t, bool >> &injection_trans, vector< size_t > *path_node_provenance=nullptr)
 Add edges between reachable nodes and split nodes at overlaps. More...
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, size_t band_padding, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void align (const Alignment &alignment, const HandleGraph &align_graph, const GSSWAligner *aligner, bool score_anchors_as_matches, size_t max_alt_alns, bool dynamic_alt_alns, size_t max_gap, double pessimistic_tail_gap_multiplier, bool simplify_topologies, size_t unmergeable_len, function< size_t(const Alignment &, const HandleGraph &)> band_padding_function, multipath_alignment_t &multipath_aln_out, SnarlManager *cutting_snarls=nullptr, SnarlDistanceIndex *dist_index=nullptr, const function< pair< id_t, bool >(id_t)> *project=nullptr, bool allow_negative_scores=false, unordered_map< handle_t, bool > *left_align_strand=nullptr)
 
void to_dot (ostream &out, const Alignment *alignment=nullptr) const
 
vector< vector< id_t > > get_connected_components () const
bool allow_negative_scores = false allow_negative_scores = false,
unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool allow_negative_scores = false allow_negative_scores = false,
unordered_map< handle_t, bool > * left_align_strand = nullptr 
- - + + diff --git a/classvg_1_1QualAdjAligner.html b/classvg_1_1QualAdjAligner.html index 382880ce483..2d465b84c9b 100644 --- a/classvg_1_1QualAdjAligner.html +++ b/classvg_1_1QualAdjAligner.html @@ -96,12 +96,12 @@ - - + + - - + + @@ -359,8 +359,8 @@

-

◆ align_global_banded()

+ +

◆ align_global_banded()

@@ -390,7 +390,13 @@

- + + + + + + + @@ -406,12 +412,12 @@

store optimal global alignment against a graph within a specified band in the Alignment object permissive banding auto detects the width of band needed so that paths can travel through every node in the graph

-

Implements vg::GSSWAligner.

+

Implements vg::GSSWAligner.

- -

◆ align_global_banded_multi()

+ +

◆ align_global_banded_multi()

@@ -453,7 +459,13 @@

- + + + + + + + @@ -469,7 +481,7 @@

store top scoring global alignments in the vector in descending score order up to a maximum number of alternate alignments (including the optimal alignment). if there are fewer than the maximum number of alignments in the return value, then the vector contains all possible alignments. the optimal alignment will be stored in both the vector and the original alignment object

-

Implements vg::GSSWAligner.

+

Implements vg::GSSWAligner.

diff --git a/functions_a.html b/functions_a.html index dea2d38f7e5..e06d5686789 100644 --- a/functions_a.html +++ b/functions_a.html @@ -332,7 +332,7 @@

- a -

align(Alignment &alignment, const HandleGraph &g, bool traceback_aln) constvg::QualAdjAlignervirtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) constvg::QualAdjAlignervirtual
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) constvg::QualAdjAlignervirtual
align_global_banded(Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) constvg::QualAdjAlignervirtual
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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) constvg::QualAdjAlignervirtual
align_internal(Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) constvg::QualAdjAlignerprotected
align_pinned(Alignment &alignment, const HandleGraph &g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) constvg::QualAdjAlignervirtual
align_pinned_multi(Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) constvg::QualAdjAlignervirtual
 
void align (Alignment &alignment, const HandleGraph &g, bool traceback_aln) const
 
void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const
 
void align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const
 
void 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
 
void 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) const
 
void 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, const unordered_map< handle_t, bool > *left_align_strand=nullptr) const
 
void align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const
 
void 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
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
bool permissive_banding = true permissive_banding = true,
const unordered_map< handle_t, bool > * left_align_strand = nullptr 
- - - -

-Macros

#define _POSIX_C_SOURCE   200809L
 
@@ -101,21 +95,6 @@

Functions

void vg_help (char **argv)
int main (int argc, char *argv[]) VG_PREFLIGHT_EVERYWHERE
 
-

Macro Definition Documentation

- -

◆ _POSIX_C_SOURCE

- -
-
- - - - -
#define _POSIX_C_SOURCE   200809L
-
- -
-

Function Documentation

◆ main()

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