#include <alignment_scorer.hpp>
Inheritance diagram for vg::QualAdjAlignmentScorer:
Public Member Functions | |
| QualAdjAlignmentScorer (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) | |
| ~QualAdjAlignmentScorer () override | |
| 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_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_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::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) | |
| ~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 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 (size_t length) const |
| 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 |
Protected Member Functions | |
| int8_t * | qual_adjusted_matrix (const int8_t *score_matrix_4x4, double gc_content, double log_base, uint32_t max_qual) const |
| int8_t * | qual_adjusted_bonuses (int8_t base_full_length_bonus, double log_base, uint32_t max_qual) const |
Protected Attributes | |
| int8_t * | qual_adj_full_length_bonuses = nullptr |
| Per-quality full-length bonus table. Owned by this class. More... | |
| Protected Attributes inherited from vg::MatrixAlignmentScorer | |
| double | log_base |
| We remember our computed log base. More... | |
Additional Inherited Members | |
| Public Attributes inherited from vg::MatrixAlignmentScorer | |
| 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 |
| 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
AlignmentScorer that scores alignments using quality-adjusted scoring.
Handles adjusting a 4x4 input scoring matrix for base quality.
Constructor & Destructor Documentation
◆ QualAdjAlignmentScorer()
| vg::QualAdjAlignmentScorer::QualAdjAlignmentScorer | ( | const int8_t * | score_matrix_4x4 = default_score_matrix, |
| int8_t | gap_open = default_gap_open, |
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| int8_t | gap_extension = default_gap_extension, |
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| int8_t | full_length_bonus = default_full_length_bonus, |
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| double | gc_content = default_gc_content |
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| ) |
◆ ~QualAdjAlignmentScorer()
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override |
Member Function Documentation
◆ qual_adjusted_bonuses()
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protected |
◆ qual_adjusted_matrix()
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protected |
◆ score_exact_match() [1/3]
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overridevirtual |
Compute the score of an exact match in the given alignment, from the given offset, of the given length.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_exact_match() [2/3]
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overridevirtual |
Compute the score of an exact match of the given sequence with the given qualities. Qualities may be ignored by some implementations.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_exact_match() [3/3]
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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.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_full_length_bonus() [1/2]
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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.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_full_length_bonus() [2/2]
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overridevirtual |
Compute the score bonus that would be achieved by a full-length alignment of the given end of the given read.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_mismatch()
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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.
Reimplemented from vg::MatrixAlignmentScorer.
◆ score_partial_alignment()
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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.
Reimplemented from vg::MatrixAlignmentScorer.
Member Data Documentation
◆ qual_adj_full_length_bonuses
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protected |
Per-quality full-length bonus table. Owned by this class.
The documentation for this class was generated from the following files:
