#include <alignment_scorer.hpp>
Public Member Functions | |
| MatrixAlignmentScorer (const int8_t *score_matrix_4x4=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) | |
| ~MatrixAlignmentScorer () override | |
| MatrixAlignmentScorer (const MatrixAlignmentScorer &)=delete | |
| MatrixAlignmentScorer & | operator= (const MatrixAlignmentScorer &)=delete |
| double | get_log_base () const override |
| Retrieve the log base value that was computed at construction. More... | |
| int32_t | score_exact_match (const Alignment &aln, size_t read_offset, size_t length) const override |
| int32_t | score_exact_match (const std::string &sequence, const std::string &base_quality) const override |
| int32_t | score_exact_match (std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override |
| int32_t | score_exact_match (const std::string &sequence) const |
| Score an exact match of unspecified sequence and the given length. More... | |
| int32_t | score_exact_match (std::string::const_iterator seq_begin, std::string::const_iterator seq_end) const |
| int32_t | score_mismatch (std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override |
| int32_t | score_mismatch (size_t length) const |
| int32_t | score_full_length_bonus (bool left_side, std::string::const_iterator seq_begin, std::string::const_iterator seq_end, std::string::const_iterator base_qual_begin) const override |
| int32_t | score_full_length_bonus (bool left_side, const Alignment &alignment) const override |
| int32_t | score_partial_alignment (const Alignment &alignment, const HandleGraph &graph, const path_t &path, std::string::const_iterator seq_begin, bool no_read_end_scoring=false) const override |
 Public Member Functions inherited from vg::EditAlignmentScorer | |
| EditAlignmentScorer (int8_t match=default_match, int8_t mismatch=default_mismatch, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus) | |
| int32_t | score_alignment (const Alignment &aln) const override |
| Score an alignment as a contiguous alignment, including full-length bonuses. More... | |
| virtual int32_t | score_gap (size_t gap_length) const |
| Returns the score of an insert or deletion of the given length. More... | |
| virtual int32_t | score_discontiguous_alignment (const Alignment &aln, const std::function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool allow_left_bonus=true, bool allow_right_bonus=true) const |
| virtual int32_t | score_contiguous_alignment (const Alignment &aln, bool allow_left_bonus=true, bool allow_right_bonus=true) const |
| Score the given alignment assuming there are no gaps between Mappings. More... | |
| virtual int32_t | remove_bonuses (const Alignment &aln, bool pinned=false, bool pin_left=false) const |
| size_t | longest_detectable_gap (const Alignment &alignment, const std::string::const_iterator &read_pos) const |
| The longest gap detectable from a read position without soft-clipping. More... | |
| size_t | longest_detectable_gap (size_t read_length, size_t read_pos) const |
| The longest gap detectable from a read position without soft-clipping, for a generic read. More... | |
| size_t | longest_detectable_gap (const Alignment &alignment) const |
| The longest gap detectable from any read position without soft-clipping. More... | |
| size_t | longest_detectable_gap (size_t read_length) const |
| The longest gap detectable from any read position without soft-clipping, for a generic read. More... | |
| Public Member Functions inherited from vg::AlignmentScorer | |
| virtual | ~AlignmentScorer ()=default |
Public Attributes | |
| int8_t * | score_matrix |
| int8_t * | nt_table |
| Char->int nt translation. Owned by this class. More... | |
| Public Attributes inherited from vg::EditAlignmentScorer | |
| int8_t | match |
| int8_t | mismatch |
| int8_t | gap_open |
| int8_t | gap_extension |
| int8_t | full_length_bonus |
Protected Attributes | |
| double | log_base |
| We remember our computed log base. More... | |
Additional Inherited Members | |
| Static Protected Member Functions inherited from vg::AlignmentScorer | |
| static double | recover_log_base (const double matrix[16], double gc_content, double tol=1e-12) |
Detailed Description
An alignment scorer that scores bassed on a score matrix.
Takes 4x4 matrices for construction, but internally uses 5x5 N-padded, GSSW-compatible matrices.
Constructor & Destructor Documentation
◆ MatrixAlignmentScorer() [1/2]
| vg::MatrixAlignmentScorer::MatrixAlignmentScorer | ( | const int8_t * | score_matrix_4x4 = 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 |
||
| ) |
Build from a 4x4 substitution matrix and gap parameters.
Fills in the generic base match and mismatch values from the matrix.
◆ ~MatrixAlignmentScorer()
|
override |
◆ MatrixAlignmentScorer() [2/2]
|
delete |
Member Function Documentation
◆ get_log_base()
|
overridevirtual |
Retrieve the log base value that was computed at construction.
Implements vg::AlignmentScorer.
◆ operator=()
|
delete |
◆ score_exact_match() [1/5]
|
overridevirtual |
Compute the score of an exact match in the given alignment, from the given offset, of the given length.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_exact_match() [2/5]
| int32_t vg::MatrixAlignmentScorer::score_exact_match | ( | const std::string & | sequence | ) | const |
Score an exact match of unspecified sequence and the given length.
◆ score_exact_match() [3/5]
|
overridevirtual |
Compute the score of an exact match of the given sequence with the given qualities. Qualities may be ignored by some implementations.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_exact_match() [4/5]
| int32_t vg::MatrixAlignmentScorer::score_exact_match | ( | std::string::const_iterator | seq_begin, |
| std::string::const_iterator | seq_end | ||
| ) | const |
◆ score_exact_match() [5/5]
|
overridevirtual |
Compute the score of an exact match of the given range of sequence with the given qualities. Qualities may be ignored by some implementations.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_full_length_bonus() [1/2]
|
overridevirtual |
Compute the score bonus that would be achieved by a full-length alignment of the given end of the given read. Does not check whether that end actually has a full-lenght alignment.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_full_length_bonus() [2/2]
|
overridevirtual |
Compute the score bonus that would be achieved by a full-length alignment of the given end of the given read.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_mismatch() [1/2]
| int32_t vg::MatrixAlignmentScorer::score_mismatch | ( | size_t | length | ) | const |
Score a mismatch of unspecified sequence of the given length. This usually produces a negative score.
◆ score_mismatch() [2/2]
|
overridevirtual |
Compute the score of a mismatch of the given range of sequence with the given qualities. Qualities may be ignored by some implementations. Note that the return value is SIGNED, and almost certainly NEGATIVE, because mismatches are bad.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
◆ score_partial_alignment()
|
overridevirtual |
Compute the score of a path against the given range of subsequence with the given qualities. The Alignment is just to find the sequence begin and end to compare to seq_begin. seq_begin is the first read base involved in the provided path to be scored.
Implements vg::EditAlignmentScorer.
Reimplemented in vg::QualAdjAlignmentScorer.
Member Data Documentation
◆ log_base
|
protected |
We remember our computed log base.
◆ nt_table
| int8_t* vg::MatrixAlignmentScorer::nt_table |
Char->int nt translation. Owned by this class.
◆ score_matrix
| int8_t* vg::MatrixAlignmentScorer::score_matrix |
5x5 GSSW-style N-padded matrix in row-major order, possibly with multiple levels. Owned by this class.
This class makes this a 5x5x1 matrix, but subclasses can make this have more dimensions.
The documentation for this class was generated from the following files:
