Fixed issues.

bbuchfink · Jun 20, 2023 · 194e174 · 194e174
1 parent 03e7f4a
commit 194e174
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 3 deletions.
diff --git a/src/align/align.cpp b/src/align/align.cpp
@@ -316,7 +316,11 @@ void align_queries(Consumer* output_file, Search::Config& cfg)
 			log_stream << "Warning: resident size (" << (res_size + last_size) << ") exceeds memory limit." << std::endl;
 
 		timer.go("Sorting trace points");
+#ifdef NDEBUG
 		ips4o::parallel::sort(hit_buf->begin(), hit_buf->end(), std::less<Search::Hit>(), config.threads_);
+#else
+		std::sort(hit_buf->begin(), hit_buf->end());
+#endif
 		statistics.inc(Statistics::TIME_SORT_SEED_HITS, timer.microseconds());
 
 #ifndef OLD

diff --git a/src/run/double_indexed.cpp b/src/run/double_indexed.cpp
@@ -306,7 +306,7 @@ static void run_query_iteration(const unsigned query_iteration,
 	if (!config.swipe_all && !config.target_indexed) {
 		timer.go("Building query histograms");
 		EnumCfg enum_cfg{ nullptr, 0, 0, options.seed_encoding, options.query_skip.get(), false, false, options.seed_complexity_cut,
-			options.soft_masking, options.minimizer_window, query_seeds_hashed.get(), false };
+			options.soft_masking, options.minimizer_window, (bool)query_seeds_hashed, false };
 		options.query->hst() = SeedHistogram(*options.query, false, &no_filter, enum_cfg);
 		timer.finish();
 	}

diff --git a/src/search/seed_complexity.cpp b/src/search/seed_complexity.cpp
@@ -39,6 +39,8 @@ bool Search::seed_is_complex(const Letter* seq, const Shape& shape, const double
 	count.fill(0);
 	for (int i = 0; i < shape.weight_; ++i) {
 		const Letter l = letter_mask(seq[shape.positions_[i]]);
+		if (l >= TRUE_AA)
+			return false;
 		++count[Reduction::reduction(l)];
 	}
 	double entropy = lnfact[shape.weight_];

diff --git a/src/search/stage0.cpp b/src/search/stage0.cpp
@@ -109,7 +109,7 @@ void search_shape(unsigned sid, int query_block, unsigned query_iteration, char
 		TaskTimer timer("Building reference seed array", true);
 		SeedArray *ref_idx;
 		const EnumCfg enum_ref{ &ref_hst.partition(), sid, sid + 1, cfg.seed_encoding, nullptr, false, false, cfg.seed_complexity_cut,
-			query_seeds_bitset.get() || query_seeds_hashed.get() ? MaskingAlgo::NONE : cfg.soft_masking,
+			query_seeds_bitset.get() || (bool)query_seeds_hashed ? MaskingAlgo::NONE : cfg.soft_masking,
 			cfg.minimizer_window, false, false };
 		if (query_seeds_bitset.get())
 			ref_idx = new SeedArray(*cfg.target, ref_hst.get(sid), range, ref_buffer, query_seeds_bitset.get(), enum_ref);
@@ -124,7 +124,7 @@ void search_shape(unsigned sid, int query_block, unsigned query_iteration, char
 		timer.go("Building query seed array");
 		SeedArray* query_idx;
 		EnumCfg enum_query{ target_seeds ? nullptr : &query_hst.partition(), sid, sid + 1, cfg.seed_encoding, cfg.query_skip.get(),
-			false, true, cfg.seed_complexity_cut, cfg.soft_masking, cfg.minimizer_window, query_seeds_hashed.get(), query_seeds_hashed.get() };
+			false, true, cfg.seed_complexity_cut, cfg.soft_masking, cfg.minimizer_window, (bool)query_seeds_hashed, (bool)query_seeds_hashed };
 		if (target_seeds)
 			query_idx = new SeedArray(*cfg.query, range, target_seeds, enum_query);
 		else