Contig stitcher: add few more tests

Author: Donaim

micall/tests/data/stitcher_plots/test_stitch_cross_alignment.svg

@@ -755,6 +755,7 @@ def test_gap_around_small_insertion(exact_aligner, visualizer):
 
     results = list(stitch_consensus(contigs))
     assert len(results) == 1
+    assert results[0].seq == "P" * 5 + "A" * 10 + "B" * 20 + "C" * 10 + "Z" * 5
     assert len(visualizer().elements) > len(contigs)
 
 
@@ -782,6 +783,50 @@ def test_gap_around_big_insertion(exact_aligner, visualizer):
 
     results = list(stitch_consensus(contigs))
     assert len(results) == 1
+    assert results[0].seq == "P" * 5 + "A" * 10 + "B" * 20 + "C" * 10 + "Z" * 5
+    assert len(visualizer().elements) > len(contigs)
+
+
+def test_stitch_with_insertion(exact_aligner, visualizer):
+    # Scenario: Contig is aligned with multiple hits, and the borders are correctly handled.
+
+    ref_seq='X' * 5 + 'A' * 10 + 'B' * 20 + 'C' * 10 + 'M' * 5
+
+    contigs = [
+        GenotypedContig(name='a',
+                        seq='P' * 5 + 'A' * 10 + 'D' * 6 + 'C' * 10 + 'Z' * 5,
+                        ref_name='testref',
+                        group_ref='testref',
+                        ref_seq=ref_seq,
+                        match_fraction=0.3,
+                        ),
+        ]
+
+    results = list(stitch_consensus(contigs))
+    assert len(results) == 1
+    assert results[0].seq == "PPPPPAAAAAAAAAADDDDDDCCCCCCCCCCZZZZZ"
+    assert len(visualizer().elements) > len(contigs)
+
+
+
+def test_stitch_cross_alignment(exact_aligner, visualizer):
+    # Scenario: Single contig is cross-aligned.
+
+    ref_seq='X' * 5 + 'A' * 10 + 'B' * 20 + 'C' * 10 + 'M' * 5
+
+    contigs = [
+        GenotypedContig(name='a',
+                        seq='P' * 5 + 'C' * 10 + 'D' * 6 + 'A' * 10 + 'Z' * 5,
+                        ref_name='testref',
+                        group_ref='testref',
+                        ref_seq=ref_seq,
+                        match_fraction=0.3,
+                        ),
+        ]
+
+    results = list(stitch_consensus(contigs))
+    assert len(results) == 1
+    assert results[0].seq == "AAAAAAAAAACCCCCCCCCC"
     assert len(visualizer().elements) > len(contigs)