Fix #12 0 cov in region with cov

inodb · Sep 10, 2015 · 5e93276 · 5e93276
1 parent fdccfe1
commit 5e93276
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Showing 2 changed files with 8 additions and 0 deletions.
diff --git a/sufam/__main__.py b/sufam/__main__.py
@@ -97,6 +97,9 @@ def get_baseparser_extended_df(sample, bp_lines, ref, alt):
                         columns=["sample"] + columns, dtype=np.object)
     bpdf[bpdf == ""] = None
 
+    # remove zero coverage rows
+    bpdf = bpdf[bpdf["cov"].astype(int) > 0]
+
     if len(bpdf) == 0:
         return None
 

diff --git a/tests/test_validation.py b/tests/test_validation.py
@@ -106,3 +106,8 @@ def test_mpileup_test3(self):
         assert_equals("+", bpdf.most_common_indel_type.iloc[0])
         assert_almost_equals(0.0139, float(bpdf.val_maf.iloc[0]), places=3)
         assert_almost_equals(0.0139, float(bpdf.most_common_al_maf.iloc[0]), places=3)
+
+    def test_0cov_regionwithcov(self):
+        test = open(ospj(DATA_PATH, "mpileup_0cov_regionwithcov.tsv")).read()
+        bpdf = sufam.__main__.get_baseparser_extended_df("test", [mpileup_parser.parse(test)], "G", "GAA")
+        assert_equals(None, bpdf)