Fix asserts when aligning an empty sequence (#383)

ratschlab · Feb 5, 2022 · d4ffe55 · d4ffe55
1 parent cbca6d6
commit d4ffe55
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 3 deletions.
diff --git a/metagraph/src/graph/alignment/aligner_extender_methods.cpp b/metagraph/src/graph/alignment/aligner_extender_methods.cpp
@@ -32,8 +32,9 @@ DefaultColumnExtender::DefaultColumnExtender(const DeBruijnGraph &graph,
                    [&](char c) { return config_.get_row(c)[c]; });
 
     std::partial_sum(partial_sums_.rbegin(), partial_sums_.rend(), partial_sums_.rbegin());
-    assert(config_.match_score(query_) == partial_sums_.front());
-    assert(config_.get_row(query_.back())[query_.back()] == partial_sums_.back());
+    assert(query_.empty() || config_.match_score(query_) == partial_sums_.front());
+    assert(query_.empty() || config_.get_row(query_.back())[query_.back()] == partial_sums_.back());
+
     partial_sums_.push_back(0);
 
     // precompute profiles to store match/mismatch scores and Cigar::Operators

diff --git a/metagraph/src/graph/alignment/aligner_seeder_methods.cpp b/metagraph/src/graph/alignment/aligner_seeder_methods.cpp
@@ -30,7 +30,7 @@ ExactSeeder::ExactSeeder(const DeBruijnGraph &graph,
 
     std::partial_sum(partial_sum_.begin(), partial_sum_.end(), partial_sum_.begin());
     assert(config_.match_score(query_) == partial_sum_.back());
-    assert(config_.get_row(query_.front())[query_.front()] == partial_sum_[1]);
+    assert(query_.empty() || config_.get_row(query_.front())[query_.front()] == partial_sum_[1]);
     assert(!partial_sum_.front());
 }
 

diff --git a/metagraph/tests/graph/test_aligner.cpp b/metagraph/tests/graph/test_aligner.cpp
@@ -96,6 +96,19 @@ TYPED_TEST(DBGAlignerTest, bad_min_cell_score) {
     ASSERT_THROW(DBGAligner<>(*graph, config), std::runtime_error);
 }
 
+TYPED_TEST(DBGAlignerTest, align_empty) {
+    size_t k = 4;
+    std::string reference = "CATTT";
+    std::string query;
+
+    auto graph = build_graph_batch<TypeParam>(k, { reference });
+    DBGAlignerConfig config(DBGAlignerConfig::dna_scoring_matrix(2, -1, -2));
+    DBGAligner<> aligner(*graph, config);
+    auto paths = aligner.align(query);
+
+    EXPECT_EQ(0ull, paths.size());
+}
+
 TYPED_TEST(DBGAlignerTest, align_sequence_much_too_short) {
     size_t k = 4;
     std::string reference = "CATTT";