Reject --align-chain up front where seed chaining cannot work

metagraph/integration_tests/test_align.py

@@ -391,6 +391,43 @@ def test_simple_align_edit_distance_all_graphs(self, representation):
             self.assertEqual(a, b)
 
 
+    def test_align_chain_requires_coordinates(self):
+        def build(mode):
+            graph = self.tempdir.name + f'/genome.MT.{mode}'
+            self._build_graph(input=TEST_DATA_DIR + '/genome.MT.fa',
+                              output=graph, k=11, repr='succinct', mode=mode)
+            return graph + '.dbg'
+
+        def annotate(graph, anno_repr):
+            prefix = graph[:-len('.dbg')]
+            self._annotate_graph(TEST_DATA_DIR + '/genome.MT.fa', graph, prefix, anno_repr)
+            return f'{prefix}.{anno_repr}.annodbg'
+
+        def align(graph, anno):
+            command = f'{METAGRAPH} align --align-chain -i {graph} -a {anno} '\
+                      f'{TEST_DATA_DIR}/genome_MT1.fq'
+            return subprocess.run(command.split(), stdout=PIPE, stderr=PIPE)
+
+        basic = build('basic')
+        canonical = build('canonical')
+
+        # no coordinates in the annotation
+        res = align(basic, annotate(basic, 'column'))
+        self.assertNotEqual(res.returncode, 0)
+        self.assertIn('--align-chain requires', res.stderr.decode())
+        self.assertEqual(res.stdout, b'')
+
+        # coordinates are not used on CANONICAL graphs
+        res = align(canonical, annotate(canonical, 'column_coord'))
+        self.assertNotEqual(res.returncode, 0)
+        self.assertIn('--align-chain requires', res.stderr.decode())
+
+        # a BASIC graph with coordinates is accepted
+        res = align(basic, annotate(basic, 'column_coord'))
+        self.assertEqual(res.returncode, 0)
+        self.assertEqual(len(res.stdout.decode().rstrip().split('\n')), 7)
+
+
 @unittest.skipUnless(PROTEIN_MODE, "These alignment tests are only for the Protein alphabet")
 class TestProteinAlign(TestingBase):
     def setUp(self):

metagraph/src/cli/align.cpp

@@ -10,6 +10,7 @@
 #include "graph/alignment/dbg_aligner.hpp"
 #include "graph/alignment/aligner_labeled.hpp"
 #include "graph/annotated_dbg.hpp"
+#include "annotation/int_matrix/base/int_matrix.hpp"
 #include "graph/graph_extensions/node_first_cache.hpp"
 #include "seq_io/sequence_io.hpp"
 #include "config/config.hpp"
@@ -382,6 +383,18 @@ int align_to_graph(Config *config) {
     if (anno_dbg_future.valid())
         anno_dbg = anno_dbg_future.get();
 
+    // Chaining needs the coordinates of the seeds, which the aligner uses only
+    // with an annotation with coordinates on a BASIC-mode graph.
+    if (config->alignment_chain
+            && (graph->get_mode() != DeBruijnGraph::BASIC || !anno_dbg
+                || !dynamic_cast<const annot::matrix::MultiIntMatrix*>(
+                        &anno_dbg->get_annotator().get_matrix()))) {
+        logger->error("--align-chain requires a BASIC-mode graph and an annotation "
+                      "with coordinates (e.g., annotate --coordinates, then "
+                      "transform_anno --anno-type column_coord)");
+        return 1;
+    }
+
     auto wrap_graph = [&](auto graph) {
         if (graph->get_mode() == DeBruijnGraph::PRIMARY) {
             graph = std::make_shared<CanonicalDBG>(graph);

metagraph/src/graph/alignment/dbg_aligner.cpp

@@ -545,7 +545,7 @@ ::align_both_directions(std::string_view forward,
 
     if (config_.chain_alignments) {
         if (!has_coordinates()) {
-            logger->error("Chaining only supported for seeds with coordinates. Skipping seed chaining.");
+            logger->error("Chaining requires seeds with coordinates");
             exit(1);
         }