Introduce the concept of relaxation

src/aligntools/cigar.py

@@ -220,6 +220,15 @@ def coordinate_mapping(self) -> CoordinateMapping:
 
         return mapping
 
+    def relax(self) -> 'Cigar':
+        """
+        Turn `CigarActions.SEQ_MATCH` and `CigarActions.MISMATCH`
+        into `CigarActions.MATCH`.
+        """
+
+        new = [(count, action.relax()) for (count, action) in self._data]
+        return Cigar(new)
+
     def to_msa(self, reference_seq: str, query_seq: str) -> Tuple[str, str]:
         """
         Constructs a multiple sequence alignment (MSA) representation
@@ -283,9 +292,9 @@ def from_msa(reference: str, query: str) -> 'Cigar':
             elif query_base == '-':
                 op = CigarActions.DELETE
             elif ref_base == query_base:
-                op = CigarActions.MATCH
+                op = CigarActions.SEQ_MATCH
             else:
-                op = CigarActions.MATCH
+                op = CigarActions.MISMATCH
 
             operations.append((1, op))
 

src/aligntools/cigar_actions.py

@@ -47,6 +47,14 @@ def parse(value: str) -> 'CigarActions':
     def __str__(self) -> str:
         return OP_MAPPING_REV[self]
 
+    def relax(self) -> 'CigarActions':
+        if self == CigarActions.SEQ_MATCH:
+            return CigarActions.MATCH
+        elif self == CigarActions.MISMATCH:
+            return CigarActions.MATCH
+        else:
+            return self
+
 
 OP_MAPPING = {
     'M': CigarActions.MATCH,

tests/test_main.py

@@ -757,7 +757,7 @@ def test_illigal_cigar_to_msa(cigar, reference_seq, query_seq):
     ]
 )
 def test_from_msa(reference, query, expected_cigar_str):
-    cigar = Cigar.from_msa(reference, query)
+    cigar = Cigar.from_msa(reference, query).relax()
     assert str(cigar) == expected_cigar_str