Don't include empty positions in VariantCalls.

cfe-lab · Jan 26, 2018 · ce92d45 · ce92d45
1 parent 774bb04
commit ce92d45
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Showing 3 changed files with 13 additions and 4 deletions.
diff --git a/pyvdrm/tests/test_vcf.py b/pyvdrm/tests/test_vcf.py
@@ -340,6 +340,15 @@ def test_init_multiple_sequences(self):
 
         self.assertEqual(expected_calls, calls)
 
+    def test_init_empty_sequence(self):
+        reference = 'ACHE'
+        sample = ['IN', 'C', '', 'E']
+        expected_calls = VariantCalls('A1IN C2C E4E')
+
+        calls = VariantCalls(reference=reference, sample=sample)
+
+        self.assertEqual(expected_calls, calls)
+
     def test_init_bad_length(self):
         reference = 'ACHE'
         sample = 'ICREL'

diff --git a/pyvdrm/vcf.py b/pyvdrm/vcf.py
@@ -38,7 +38,8 @@ def __new__(cls, text=None, reference=None, sample=None):
             mutation_sets = {MutationSet(pos=i, variants=alt, wildtype=ref)
                              for i, (alt, ref) in enumerate(zip(sample,
                                                                 reference),
-                                                            1)}
+                                                            1)
+                             if alt}
         positions = set()
         for mutation_set in mutation_sets:
             if mutation_set.pos in positions:

diff --git a/setup.py b/setup.py
@@ -2,7 +2,7 @@
 
 setup(
     name='pyvdrm',
-    version='0.3.0',
+    version='0.3.1',
     description='',
 
     url='',
@@ -14,5 +14,4 @@
     install_requires=['pyparsing'],
 
     setup_requires=['pytest-runner'],
-    tests_require=['pytest']
-)
+    tests_require=['pytest'])