vg
tools for working with variation graphs
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#include <banded_global_aligner.hpp>
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 () | |
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) |
Use DP to fill the band with alignment scores. More... | |
void | traceback (const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, matrix_t start_mat, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf) |
Traceback through the band after using DP to fill it. More... | |
void | print_full_matrices (const HandleGraph &graph) |
Debugging function. More... | |
void | print_rectangularized_bands (const HandleGraph &graph) |
Debugging function. More... | |
Private Member Functions | |
void | traceback_internal (const HandleGraph &graph, BABuilder &builder, AltTracebackStack &traceback_stack, int64_t start_row, int64_t start_col, matrix_t start_mat, bool in_lead_gap, int8_t *score_mat, int8_t *nt_table, int8_t gap_open, int8_t gap_extend, bool qual_adjusted, IntType min_inf) |
void | print_matrix (const HandleGraph &graph, matrix_t which_mat) |
Debugging function. More... | |
void | print_band (const HandleGraph &graph, matrix_t which_mat) |
Debugging function. More... | |
Private Attributes | |
int64_t | top_diag |
The diagonals in the DP matrix that the band passes through with the bottom index inclusive. More... | |
int64_t | bottom_diag |
handle_t | node |
Alignment & | alignment |
int64_t | cumulative_seq_len |
Length of shortest sequence leading to matrix from a source node. More... | |
vector< BAMatrix * > | seeds |
Matrices for nodes with edges into this node. More... | |
IntType * | match |
DP matrix. More... | |
IntType * | insert_col |
DP matrix. More... | |
IntType * | insert_row |
DP matrix. More... | |
Friends | |
class | BABuilder |
class | AltTracebackStack |
Represents the band from the DP matrix for one node in the graph
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 | ||
) |
vg::BandedGlobalAligner< IntType >::BAMatrix::~BAMatrix | ( | ) |
void vg::BandedGlobalAligner< IntType >::BAMatrix::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 | ||
) |
Use DP to fill the band with alignment scores.
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Debugging function.
void vg::BandedGlobalAligner< IntType >::BAMatrix::print_full_matrices | ( | const HandleGraph & | graph | ) |
Debugging function.
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Debugging function.
void vg::BandedGlobalAligner< IntType >::BAMatrix::print_rectangularized_bands | ( | const HandleGraph & | graph | ) |
Debugging function.
void vg::BandedGlobalAligner< IntType >::BAMatrix::traceback | ( | const HandleGraph & | graph, |
BABuilder & | builder, | ||
AltTracebackStack & | traceback_stack, | ||
matrix_t | start_mat, | ||
int8_t * | score_mat, | ||
int8_t * | nt_table, | ||
int8_t | gap_open, | ||
int8_t | gap_extend, | ||
bool | qual_adjusted, | ||
IntType | min_inf | ||
) |
Traceback through the band after using DP to fill it.
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Length of shortest sequence leading to matrix from a source node.
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DP matrix.
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DP matrix.
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DP matrix.
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Matrices for nodes with edges into this node.
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The diagonals in the DP matrix that the band passes through with the bottom index inclusive.