Contig stitcher: remove unused aligned_seq field

micall/core/contig_stitcher.py

@@ -71,12 +71,6 @@ def __init__(self, query: GenotypedContig, alignment: CigarHit):
             matched_fraction = query.matched_fraction)
 
 
-    @cached_property
-    def aligned_seq(self):
-        ref_msa, query_msa = self.alignment.to_msa(self.query.ref_seq, self.query.seq)
-        return ''.join((c for c in query_msa if c != '-'))
-
-
     def cut_reference(self, cut_point: float) -> Tuple['AlignedContig', 'AlignedContig']:
         """ Cuts this alignment in two parts with cut_point between them. """
 

micall/tests/test_contig_stitcher.py

@@ -440,7 +440,7 @@ def test_stitching_contig_with_small_covered_gap(exact_aligner):
 
     results = list(split_contigs_with_gaps(contigs))
 
-    assert all(x.seq == x.aligned_seq for x in results)
+    assert all(x.seq == x.lstrip_query().rstrip_query().seq for x in results)
 
     assert set(map(lambda x: x.seq, contigs)) \
         == set(map(lambda x: x.seq, results))
@@ -463,10 +463,10 @@ def test_stitching_partial_align(exact_aligner):
     for result in results:
         assert any(result.seq in contig.seq for contig in contigs)
 
-    assert all(x.seq != x.aligned_seq for x in results)
+    assert all(x.seq != x.lstrip_query().rstrip_query().seq for x in results)
 
     assert set(map(lambda x: x.seq, contigs)) \
-        != set(map(lambda x: x.aligned_seq, results))
+        != set(map(lambda x: x.lstrip_query().rstrip_query().seq, results))
 
 
 def test_partial_align_consensus(exact_aligner):
@@ -513,7 +513,7 @@ def test_stitching_partial_align_multiple_sequences(exact_aligner):
         assert any(result.seq in contig.seq for contig in contigs)
 
     assert set(map(lambda x: x.seq, contigs)) \
-        != set(map(lambda x: x.aligned_seq, results))
+        != set(map(lambda x: x.lstrip_query().rstrip_query().seq, results))
 
 
 def test_partial_align_consensus_multiple_sequences(exact_aligner):