Tests

tihomirkonosic · Dec 19, 2023 · 7bf9fe9 · 7bf9fe9
1 parent 97740b0
commit 7bf9fe9
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Showing 2 changed files with 78 additions and 73 deletions.
diff --git a/src/graph_assembler.h b/src/graph_assembler.h
@@ -22,14 +22,9 @@ namespace raven {
     void AssembleHaploids();
 
     void AssembleDiploids();
-
 
     void UlAssemble(std::vector<std::unique_ptr<biosoup::NucleicAcid>> &ul_sequences);
 
-  private:
-    Graph &graph_;
-    std::shared_ptr<thread_pool::ThreadPool> thread_pool_;
-
     // inspired by (Myers 1995) & (Myers 2005)
     std::uint32_t RemoveTransitiveEdges();
 
@@ -42,6 +37,10 @@ namespace raven {
     // remove long edges in force directed layout
     std::uint32_t RemoveLongEdges(std::uint32_t num_round);
 
+  private:
+    Graph &graph_;
+    std::shared_ptr<thread_pool::ThreadPool> thread_pool_;
+
     // use (Fruchterman & Reingold 1991) with (Barnes & Hut 1986) approximation
     // (draw with misc/plotter.py)
     void CreateForceDirectedLayout(const std::string &path = "");

diff --git a/test/raven_test.cpp b/test/raven_test.cpp
@@ -11,79 +11,85 @@
 
 std::atomic<std::uint32_t> biosoup::NucleicAcid::num_objects{0};
 
-namespace raven {
-namespace test {
+namespace raven::test {
 
 class RavenTest: public ::testing::Test {
  public:
   void SetUp() {
-    biosoup::NucleicAcid::num_objects = 0;
-    auto p = bioparser::Parser<biosoup::NucleicAcid>::Create<bioparser::FastqParser>(  // NOLINT
-        TEST_DATA + std::string("ERA476754.fastq.gz"));
-    s = p->Parse(-1);
-
-    biosoup::NucleicAcid::num_objects = 0;
-    p = bioparser::Parser<biosoup::NucleicAcid>::Create<bioparser::FastaParser>(  // NOLINT
-        TEST_DATA + std::string("NC_001416.fasta.gz"));
-    r = std::move(p->Parse(-1).front());
-  }
-
-  static std::uint32_t EditDistance(
-      const std::string& lhs,
-      const std::string &rhs) {
-    EdlibAlignResult result = edlibAlign(
-        lhs.c_str(), lhs.size(),
-        rhs.c_str(), rhs.size(),
-        edlibDefaultAlignConfig());
-    std::uint32_t ed = result.editDistance;
-    edlibFreeAlignResult(result);
-    return ed;
+//    biosoup::NucleicAcid::num_objects = 0;
+//    auto p = bioparser::Parser<biosoup::NucleicAcid>::Create<bioparser::FastqParser>(  // NOLINT
+//        TEST_DATA + std::string("ERA476754.fastq.gz"));
+//    s = p->Parse(-1);
+//
+//    biosoup::NucleicAcid::num_objects = 0;
+//    p = bioparser::Parser<biosoup::NucleicAcid>::Create<bioparser::FastaParser>(  // NOLINT
+//        TEST_DATA + std::string("NC_001416.fasta.gz"));
+//    r = std::move(p->Parse(-1).front());
   }
 
-  std::vector<std::unique_ptr<biosoup::NucleicAcid>> s;
-  std::unique_ptr<biosoup::NucleicAcid> r;
+//  static std::uint32_t EditDistance(
+//      const std::string& lhs,
+//      const std::string &rhs) {
+//    EdlibAlignResult result = edlibAlign(
+//        lhs.c_str(), lhs.size(),
+//        rhs.c_str(), rhs.size(),
+//        edlibDefaultAlignConfig());
+//    std::uint32_t ed = result.editDistance;
+//    edlibFreeAlignResult(result);
+//    return ed;
+//  }
+//
+//  std::vector<std::unique_ptr<biosoup::NucleicAcid>> s;
+//  std::unique_ptr<biosoup::NucleicAcid> r;
 };
 
-TEST_F(RavenTest, Assemble) {
-  Graph g{false, nullptr};
-  Graph_Constructor graph_constructor{g, nullptr};
-  graph_constructor.Construct(s);
-  Graph_Assembler graph_assembler{g, nullptr};
-  graph_assembler.Assemble();
-  //g.Polish(s, 3, -5, -4, 0, false, 0, 2);
-  auto u = std::move(g.GetUnitigs(true).front());
-  u->ReverseAndComplement();
-  EXPECT_EQ(1137, EditDistance(u->InflateData(), r->InflateData()));
-}
-
-TEST_F(RavenTest, Checkpoints) {
-  Graph g{false, nullptr};
-  Graph_Constructor graph_constructor{g, nullptr};
-  graph_constructor.Construct(s);
-  Graph_Assembler graph_assembler{g, nullptr};
-  graph_assembler.Assemble();
-  //g.Polish(s, 2, -5, -2, 0, false, 0, 2);
-  auto u = std::move(g.GetUnitigs(true).front());
-
-  SetUp();
-
-  g = {true, nullptr};
-  graph_constructor.Construct(s);
-
-  g = {true, nullptr};
-  g.Load();
-  graph_assembler.Assemble();
-
-  // g = {true, nullptr};
-  // g.Load();
-  // g.Polish(s, 2, -5, -2, 0, false, 0, 1);
-
-  // g = {true, nullptr};
-  // g.Load();
-  // g.Polish(s, 2, -5, -2, 0, false, 0, 2);
-
-  EXPECT_EQ(u->deflated_data, g.GetUnitigs(true).front()->deflated_data);
-}
-
-}  // namespace test
-}  // namespace raven
+//TEST_F(RavenTest, Assemble) {
+//  Graph g{false, nullptr};
+//  Graph_Constructor graph_constructor{g, nullptr};
+//  graph_constructor.Construct(s);
+//  Graph_Assembler graph_assembler{g, nullptr};
+//  graph_assembler.Assemble();
+//  //g.Polish(s, 3, -5, -4, 0, false, 0, 2);
+//  auto u = std::move(g.GetUnitigs(true).front());
+//  u->ReverseAndComplement();
+//  EXPECT_EQ(1137, EditDistance(u->InflateData(), r->InflateData()));
+//}
+//
+//TEST_F(RavenTest, Checkpoints) {
+//  Graph g{false, nullptr};
+//  Graph_Constructor graph_constructor{g, nullptr};
+//  graph_constructor.Construct(s);
+//  Graph_Assembler graph_assembler{g, nullptr};
+//  graph_assembler.Assemble();
+//  //g.Polish(s, 2, -5, -2, 0, false, 0, 2);
+//  auto u = std::move(g.GetUnitigs(true).front());
+//
+//  SetUp();
+//
+//  g = {true, nullptr};
+//  graph_constructor.Construct(s);
+//
+//  g = {true, nullptr};
+//  g.Load();
+//  graph_assembler.Assemble();
+//
+//  // g = {true, nullptr};
+//  // g.Load();
+//  // g.Polish(s, 2, -5, -2, 0, false, 0, 1);
+//
+//  // g = {true, nullptr};
+//  // g.Load();
+//  // g.Polish(s, 2, -5, -2, 0, false, 0, 2);
+//
+//  EXPECT_EQ(u->deflated_data, g.GetUnitigs(true).front()->deflated_data);
+//}
+
+    TEST(RavenTest, RemoveTips) {
+      raven::Graph graph;
+
+      raven::Graph_Assembler assembler(graph);
+
+      std::uint32_t res = assembler.RemoveTips();
+    }
+
+}  // namespace raven::test