From 3a013b0d3adcf889aaff772f80065afa2e91e7b1 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Fri, 11 Oct 2024 14:56:17 -0700
Subject: [PATCH] Add tests for CigarHit.parse

---
 src/aligntools/cigar_hit.py  | 18 +++++++-----------
 src/aligntools/exceptions.py |  2 +-
 tests/test_main.py           | 32 ++++++++++++++++++++++++++++++++
 3 files changed, 40 insertions(+), 12 deletions(-)

diff --git a/src/aligntools/cigar_hit.py b/src/aligntools/cigar_hit.py
index 1577870..370db93 100644
--- a/src/aligntools/cigar_hit.py
+++ b/src/aligntools/cigar_hit.py
@@ -339,7 +339,7 @@ def translate(self, reference_delta: int, query_delta: int) -> 'CigarHit':
                         q_ei=self.q_ei + query_delta)
 
     @staticmethod
-    def parse_cigar_hit(string: str) -> 'CigarHit':
+    def parse(string: str) -> 'CigarHit':
         """
         Parses a string representation of a CigarHit
         and returns a CigarHit object.
@@ -357,16 +357,12 @@ def parse_cigar_hit(string: str) -> 'CigarHit':
         if not match:
             raise ex.ParseError(f"Invalid CigarHit string format: {string!r}.")
 
-        try:
-            # Extracting components from the matched regex groups
-            cigar_str = match.group('cigar')
-            q_st = int(match.group('q_st'))
-            q_ei = int(match.group('q_ei'))
-            r_st = int(match.group('r_st'))
-            r_ei = int(match.group('r_ei'))
-        except ValueError as e:
-            raise ex.ParseError(f"Error parsing indices in: {string!r}.") \
-                from e
+        # Extracting components from the matched regex groups
+        cigar_str = match.group('cigar')
+        q_st = int(match.group('q_st'))
+        q_ei = int(match.group('q_ei'))
+        r_st = int(match.group('r_st'))
+        r_ei = int(match.group('r_ei'))
 
         # Validating that start indices
         # are less than or equal to end indices.
diff --git a/src/aligntools/exceptions.py b/src/aligntools/exceptions.py
index dad3443..90a975e 100644
--- a/src/aligntools/exceptions.py
+++ b/src/aligntools/exceptions.py
@@ -20,7 +20,7 @@ class MSALengthError(IndexError, CigarError):
     pass
 
 
-class InvalidOperationError(ValueError, CigarError):
+class InvalidOperationError(ParseError, CigarError):
     """Exception raised for invalid operations within CIGAR strings."""
     pass
 
diff --git a/tests/test_main.py b/tests/test_main.py
index 8359d7d..5cb3717 100644
--- a/tests/test_main.py
+++ b/tests/test_main.py
@@ -1090,3 +1090,35 @@ def test_cigar_hit_serialization():
     hit = parsed_hit("3M2I3D2M@1->1")
     assert repr(hit) \
         == "CigarHit(Cigar('3M2I3D2M'), r_st=1, r_ei=8, q_st=1, q_ei=7)"
+
+
+@pytest.mark.parametrize(
+    "hit_str, expected",
+    [
+        ("3M@[0,2]->[0,2]",
+         CigarHit(Cigar.coerce("3M"), 0, 2, 0, 2)),
+        ("3M2I3D2M@[1,7]->[1,8]",
+         CigarHit(Cigar.coerce("3M2I3D2M"), 1, 8, 1, 7)),
+        ("5M10I5D@[5,19]->[5,14]",
+         CigarHit(Cigar.coerce("5M10I5D"), 5, 14, 5, 19)),
+    ]
+)
+def test_parse_cigar_hit_valid(hit_str, expected):
+    result = CigarHit.parse(hit_str)
+    assert result == expected
+
+
+@pytest.mark.parametrize(
+    "hit_str",
+    [
+        "whatever",
+        "3K@[0,2]->[0,2]",
+        "3K@[a,b]->[c,d]",
+        "3K@[30,10]->[1,5]",
+        "3K@[3,10]->[20,5]",
+        "3K@[30,10]->[20,5]",
+    ]
+)
+def test_parse_cigar_hit_invalid(hit_str):
+    with pytest.raises(ex.ParseError):
+        CigarHit.parse(hit_str)