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Sort minimizers by score in Giraffe single-end mode #4351

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Jul 19, 2024
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Sort minimizers by score in Giraffe single-end mode #4351

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11 changes: 7 additions & 4 deletions src/minimizer_mapper.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -589,10 +589,13 @@ vector<Alignment> MinimizerMapper::map_from_extensions(Alignment& aln) {
return aln.sequence();
});


// Minimizers sorted by score in descending order.
std::vector<Minimizer> minimizers = this->find_minimizers(aln.sequence(), funnel);

// Minimizers sorted by position
std::vector<Minimizer> minimizers_in_read = this->find_minimizers(aln.sequence(), funnel);
// Indexes of minimizers, sorted into score order, best score first
std::vector<size_t> minimizer_score_order = sort_minimizers_by_score(minimizers_in_read);
// Minimizers sorted by best score first
VectorView<Minimizer> minimizers{minimizers_in_read, minimizer_score_order};

// Find the seeds and mark the minimizers that were located.
vector<Seed> seeds = this->find_seeds(minimizers, aln, funnel);

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