vg
tools for working with variation graphs
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#include <aligner.hpp>
Public Member Functions | |
void | set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length) |
Set all the aligner scoring parameters and create the stored aligner instances. More... | |
void | load_scoring_matrix (std::ifstream &matrix_stream) |
Load a scoring amtrix from a file to set scores. More... | |
Public Attributes | |
bool | adjust_alignments_for_base_quality = false |
Protected Member Functions | |
AlignerClient (double gc_content_estimate=vg::default_gc_content) | |
const GSSWAligner * | get_aligner (bool have_qualities=true) const |
const QualAdjAligner * | get_qual_adj_aligner () const |
const Aligner * | get_regular_aligner () const |
Private Attributes | |
unique_ptr< QualAdjAligner > | qual_adj_aligner |
unique_ptr< Aligner > | regular_aligner |
double | gc_content_estimate |
Holds a set of alignment scores, and has methods to produce aligners of various types on demand, using those scores. Provides a get_aligner() method to get ahold of a useful, possibly quality-adjusted Aligner. Base functionality that is shared between alignment and surjections
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Create an AlignerClient, which creates the default aligner instances, which can depend on a GC content estimate.
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Get the appropriate aligner to use, based on adjust_alignments_for_base_quality. By setting have_qualities to false, you can force the non-quality-adjusted aligner, for reads that lack quality scores.
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void AlignerClient::load_scoring_matrix | ( | std::ifstream & | matrix_stream | ) |
Load a scoring amtrix from a file to set scores.
void AlignerClient::set_alignment_scores | ( | int8_t | match, |
int8_t | mismatch, | ||
int8_t | gap_open, | ||
int8_t | gap_extend, | ||
int8_t | full_length_bonus, | ||
uint32_t | xdrop_max_gap_length = default_xdrop_max_gap_length |
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Set all the aligner scoring parameters and create the stored aligner instances.
bool vg::AlignerClient::adjust_alignments_for_base_quality = false |
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