#include <deletion_aligner.hpp>
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vector< vector< handle_t > > | run_dp (const HandleGraph &graph, int32_t max_tracebacks) const |
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pair< vector< size_t >, vector< pair< size_t, size_t > > > | min_dists (const vector< handle_t > &order, const unordered_map< handle_t, size_t > &index_of, const HandleGraph &graph) const |
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vector< vector< handle_t > > | traceback (const vector< handle_t > &order, const unordered_map< handle_t, size_t > &index_of, const HandleGraph &graph, const vector< size_t > &dists, const vector< pair< size_t, size_t > > &sinks, size_t max_tracebacks) const |
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void | trace_to_alignment (Alignment &aln, const vector< handle_t > &trace, const HandleGraph &graph) const |
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◆ DeletionAligner() [1/2]
vg::DeletionAligner::DeletionAligner |
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int8_t | gap_open, |
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int8_t | gap_extension ) |
◆ DeletionAligner() [2/2]
vg::DeletionAligner::DeletionAligner |
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◆ ~DeletionAligner()
vg::DeletionAligner::~DeletionAligner |
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◆ align()
◆ align_multi()
◆ min_dists()
pair< vector< size_t >, vector< pair< size_t, size_t > > > vg::DeletionAligner::min_dists |
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const vector< handle_t > & | order, |
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const unordered_map< handle_t, size_t > & | index_of, |
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const HandleGraph & | graph ) const |
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◆ run_dp()
vector< vector< handle_t > > vg::DeletionAligner::run_dp |
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const HandleGraph & | graph, |
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int32_t | max_tracebacks ) const |
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◆ trace_to_alignment()
◆ traceback()
vector< vector< handle_t > > vg::DeletionAligner::traceback |
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const vector< handle_t > & | order, |
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const unordered_map< handle_t, size_t > & | index_of, |
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const HandleGraph & | graph, |
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const vector< size_t > & | dists, |
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const vector< pair< size_t, size_t > > & | sinks, |
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size_t | max_tracebacks ) const |
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◆ gap_extension
int32_t vg::DeletionAligner::gap_extension |
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◆ gap_open
int32_t vg::DeletionAligner::gap_open |
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The documentation for this class was generated from the following files: