Merge branch 'release/0.3.3'

setup.py

@@ -43,7 +43,7 @@
     # For a discussion on single-sourcing the version across setup.py and the
     # project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='0.3.2',  # Required
+    version='0.3.3',  # Required
 
     # This is a one-line description or tagline of what your project does. This
     # corresponds to the "Summary" metadata field:

tests/conftest.py

@@ -2,6 +2,7 @@
 
 from zorp import parsers
 
+
 ##
 # Sample preconfigured parsers that work with the data in these test suites
 # These were defined at a time before optional columns were introduced, so in practice many of our tests have the

tests/test_parsers.py

@@ -219,6 +219,18 @@ def test_parse_marker_fails_for_invalid_format(self):
         with pytest.raises(exceptions.LineParseException, match='marker format'):
             parser_utils.parse_marker(val, test=False)
 
+    def test_parse_marker_handles_various_formats(self):
+        scenarios = [
+            ["chr1:100_A/C", ("1", "100", "A", "C")],
+            ["1:100:A:C", ("1", "100", "A", "C")],
+            ["chr1:100", ("1", "100", None, None)],
+            ["1-100-A-C", ("1", "100", "A", "C")],
+            ["1-100-A-C_AVOCADO", ("1", "100", "A", "C")],
+        ]
+        for input, expected in scenarios:
+            result = parser_utils.parse_marker(input)
+            assert result == expected, "Parsed {}".format(input)
+
     def test_pval_to_log_sidesteps_python_underflow(self):
         val = '1.93e-780'
         res = parser_utils.parse_pval_to_log(val, is_neg_log=False)

zorp/__init__.py

@@ -1,6 +1,6 @@
 from distutils.version import LooseVersion
 
-__version__ = '0.3.2'
+__version__ = '0.3.3'
 __version_info__ = tuple(LooseVersion(__version__).version)
 
 __all__ = [

zorp/parser_utils.py

@@ -15,7 +15,7 @@
     pass
 
 
-REGEX_MARKER = re.compile(r'^(?:chr)?([a-zA-Z0-9]+?):(\d+)[_:]?(\w+)?[/:|]?([^_]+)?_?(.*)?')
+REGEX_MARKER = re.compile(r'^(?:chr)?([a-zA-Z0-9]+?)[_:-](\d+)[_:|-]?(\w+)?[/_:|-]?([^_]+)?_?(.*)?')
 REGEX_PVAL = re.compile(r'([\d.\-]+)([\sxeE]*)([0-9\-]*)')