Update

metagraph/integration_tests/base.py

@@ -6,12 +6,14 @@
 
 script_path = os.path.dirname(os.path.realpath(__file__))
 
-USE_GDB = False
 METAGRAPH_EXE = f'{os.getcwd()}/metagraph'
-GDB_PREFIX = 'gdb -ex run -ex quit --args ' if USE_GDB else ''
-METAGRAPH = GDB_PREFIX + METAGRAPH_EXE
 DNA_MODE = os.readlink(METAGRAPH_EXE).endswith("_DNA")
 PROTEIN_MODE = os.readlink(METAGRAPH_EXE).endswith("_Protein")
+METAGRAPH = METAGRAPH_EXE
+
+def update_prefix(PREFIX):
+    global METAGRAPH
+    METAGRAPH = PREFIX + METAGRAPH_EXE
 
 TEST_DATA_DIR = os.path.join(script_path, '..', 'tests', 'data')
 

metagraph/integration_tests/main.py

@@ -5,6 +5,7 @@
 import sys
 import argparse
 from helpers import TimeLoggingTestResult
+from base import update_prefix
 
 
 """Run all integration tests"""
@@ -31,8 +32,12 @@ def create_test_suite(filter_pattern="*"):
     try:
         parser = argparse.ArgumentParser(description='Metagraph integration tests.')
         parser.add_argument('--test_filter', dest='filter', type=str, default="*",
-                            help='filter test cases (default: run all)')
+                    help='filter test cases (default: run all)')
+        parser.add_argument('--gdb', dest='use_gdb', action='store_true',
+                    help='run metagraph with gdb')
         args = parser.parse_args()
+        if args.use_gdb:
+            update_prefix('gdb -ex run -ex bt -ex quit --args ')
 
         result = unittest.TextTestRunner(
             resultclass=TimeLoggingTestResult

metagraph/src/annotation/binary_matrix/row_diff/row_diff.cpp

@@ -25,7 +25,7 @@ node_index row_diff_successor(const graph::DeBruijnGraph &graph,
                 succ = adjacent_node;
             }
         });
-        assert(succ != graph::DeBruijnGraph::npos && "a row diff successor must exist");
+        assert(graph.in_graph(succ) && "a row diff successor must exist");
         return succ;
     }
 }
@@ -81,22 +81,22 @@ IRowDiff::get_rd_ids(const std::vector<BinaryMatrix::Row> &row_ids) const {
         node_index node = graph::AnnotatedSequenceGraph::anno_to_graph_index(row);
 
         while (true) {
-            if (graph_->in_graph(node)) {
-                row = graph::AnnotatedSequenceGraph::graph_to_anno_index(node);
+            assert(graph_->in_graph(node));
+            row = graph::AnnotatedSequenceGraph::graph_to_anno_index(node);
 
-                auto [it, is_new] = node_to_rd.try_emplace(row, node_to_rd.size());
-                rd_paths_trunc[i].push_back(it.value());
+            auto [it, is_new] = node_to_rd.try_emplace(row, node_to_rd.size());
+            rd_paths_trunc[i].push_back(it.value());
 
-                // If a node had been reached before, we interrupt the diff path.
-                // The annotation for that node will have been reconstructed earlier
-                // than for other nodes in this path as well. Thus, we will start
-                // reconstruction from that node and don't need its successors.
-                if (!is_new)
-                    break;
+            // If a node had been reached before, we interrupt the diff path.
+            // The annotation for that node will have been reconstructed earlier
+            // than for other nodes in this path as well. Thus, we will start
+            // reconstruction from that node and don't need its successors.
+            if (!is_new)
+                break;
+
+            if (anchor_[row])
+                break;
 
-                if (anchor_[row])
-                    break;
-            }
             if (fork_succ_.size()) {
                 node = row_diff_successor(*graph_, node, fork_succ_);
             } else { // Only happens in DBGSuccinct

metagraph/src/annotation/binary_matrix/row_diff/row_diff.hpp

@@ -31,6 +31,7 @@ const std::string kRowDiffForkSuccExt = ".rd_succ";
 
 const size_t RD_PATH_RESERVE_SIZE = 2;
 
+
 class IRowDiff {
   public:
     typedef bit_vector_small anchor_bv_type;

metagraph/src/annotation/row_diff_builder.cpp

@@ -513,7 +513,6 @@ void assign_anchors(const graph::DeBruijnGraph &graph,
             [&](int32_t count) {
                 // check if the reduction is negative
                 if (count < 0) {
-                    logger->error("anchoring {}", to_node(i));
                     anchors_bv[to_node(i)] = true;
                 }
                 i++;

metagraph/tests/annotation/test_converters.cpp

@@ -299,9 +299,9 @@ TEST(RowDiff, ConvertFromColumnCompressedSameLabels) {
             EXPECT_EQ(labels.size() * expected_relations[max_depth - 1],
                       annotator.num_relations());
 
-            for (uint32 i = 0; i < annotator.num_objects(); ++i) {
-                ASSERT_THAT(annotator.get_labels(i), ContainerEq(labels));
-            }
+            graph->call_nodes([&](uint32_t node_idx) {
+                ASSERT_THAT(annotator.get_labels(node_idx - 1), ContainerEq(labels));
+            });
         }
     }
     std::filesystem::remove_all(dst_dir);
@@ -353,9 +353,9 @@ TEST(RowDiff, ConvertFromColumnCompressedSameLabelsMultipleColumns) {
                 ASSERT_EQ(graph->max_index(), annotator.num_objects());
                 EXPECT_EQ(expected_relations[max_depth - 1], annotator.num_relations());
 
-                for (uint32 idx = 0; idx < annotator.num_objects(); ++idx) {
-                    ASSERT_THAT(annotator.get_labels(idx), ElementsAre(labels[i]));
-                }
+                graph->call_nodes([&](uint32_t node_idx) {
+                    ASSERT_THAT(annotator.get_labels(node_idx - 1), ElementsAre(labels[i]));
+                });
             }
         }
     }