Sort minimizers by score in Giraffe single-end mode

Apparently in 40bf613 I meant to keep the minimizers sorted by score in single-end mapping mode, but when #3810 actually merged it changed the order that find_minimizers returns results in to read order and added a score sort to the paired-end non-chaining codepath but not the single-end non-chaining codepath.

This should restore the vg 1.44.0 behavior of taking or not taking identical minimizers all across the read, and also of prioritizing minimizers to take by score, in single-end mode.

src/minimizer_mapper.cpp

@@ -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);