Cigar tools: make CigarHit immutable

micall/core/contig_stitcher.py

@@ -212,7 +212,7 @@ def align_to_reference(contig) -> Iterable[GenotypedContig]:
         yield contig
         return
 
-    hits_array = [CigarHit(x.cigar, x.r_st, x.r_en - 1, x.q_st, x.q_en - 1) for x in alignments]
+    hits_array = [CigarHit(Cigar.coerce(x.cigar), x.r_st, x.r_en - 1, x.q_st, x.q_en - 1) for x in alignments]
     connected = connect_cigar_hits(hits_array)
 
     logger.info("Contig %r aligned in %s parts.", contig.name, len(connected),

micall/utils/cigar_tools.py

@@ -4,7 +4,7 @@
 
 from math import ceil, floor
 import re
-from typing import Container, Tuple, Iterable, Optional, Set, Dict, List
+from typing import Container, Tuple, Iterable, Optional, Set, Dict, List, Union
 from dataclasses import dataclass
 from functools import cached_property, reduce
 from itertools import chain, dropwhile
@@ -152,7 +152,7 @@ def __init__(self, data) -> None:
 
 
     @staticmethod
-    def coerce(obj):
+    def coerce(obj: Union['Cigar', str, Iterable[Tuple[int, CigarActions]]]):
         if isinstance(obj, Cigar):
             return obj
 
@@ -437,7 +437,7 @@ def __str__(self):
         return ''.join('{}{}'.format(num, Cigar.operation_to_str(op)) for num, op in self._data)
 
 
-@dataclass
+@dataclass(frozen=True)
 class CigarHit:
     """
     This class provides an abstraction over the complex details involved in working with sequence alignments
@@ -461,8 +461,6 @@ class CigarHit:
 
 
     def __post_init__(self):
-        self.cigar = Cigar.coerce(self.cigar)
-
         if self.ref_length != self.cigar.ref_length:
             raise ValueError(f"CIGAR string maps {self.cigar.ref_length}"
                              f" reference positions, but CIGAR hit range is {self.ref_length}")