Merge pull request #249 from ernfrid/classifier_pos

Update POS field in INFO when creating BNDs
hall-lab · Mar 9, 2018 · 8b054fe · 8b054fe
2 parents a388644 + 8b5cd13
commit 8b054fe
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Showing 5 changed files with 10 additions and 19 deletions.
diff --git a/svtools/sv_classifier.py b/svtools/sv_classifier.py
@@ -63,6 +63,7 @@ def to_bnd_strings(var, fixed_gts):
     var.info['CIPOS95'] = old_ciend95
     var.info['CIEND95'] = old_cipos95
     var.pos = old_end
+    var.info['POS'] = old_end
     var.info['SECONDARY'] = True
     if old_type == 'DEL':
         var.alt = ']%s:%s]N' % (var.chrom, old_pos)

diff --git a/tests/reclassifier_tests.py b/tests/reclassifier_tests.py
@@ -33,13 +33,10 @@ def test_integration_nb(self):
             expected_lines[1] = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
             produced_lines = open(temp_output_path).readlines()
             diff = difflib.unified_diff(produced_lines, expected_lines, fromfile=temp_output_path, tofile=expected_result)
+            os.remove(temp_output_path)
+            os.remove(diags_file)
             result = ''.join(diff)
-            if result != '':
-                for line in result:
-                    sys.stdout.write(line)
-                self.assertFalse(result)
-        os.remove(temp_output_path)
-        os.remove(diags_file)
+            self.assertEqual(result, '')
 
     def test_integration_ls(self):
         test_directory = os.path.dirname(os.path.abspath(__file__))
@@ -62,13 +59,10 @@ def test_integration_ls(self):
             expected_lines[1] = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
             produced_lines = open(temp_output_path).readlines()
             diff = difflib.unified_diff(produced_lines, expected_lines, fromfile=temp_output_path, tofile=expected_result)
+            os.remove(temp_output_path)
+            os.remove(diags_file)
             result = ''.join(diff)
-            if result != '':
-                for line in result:
-                   sys.stdout.write(line)
-                self.assertFalse(result)
-        os.remove(temp_output_path)
-        os.remove(diags_file)
+            self.assertEqual(result, '')
 
 
 
@@ -92,14 +86,10 @@ def test_integration_hyb(self):
             expected_lines[1] = '##fileDate=' + time.strftime('%Y%m%d') + '\n'
             produced_lines = open(temp_output_path).readlines()
             diff = difflib.unified_diff(produced_lines, expected_lines, fromfile=temp_output_path, tofile=expected_result)
+            os.remove(temp_output_path)
+            os.remove(diags_file)
             result = ''.join(diff)
-            if result != '':
-                for line in result:
-                    sys.stdout.write(line)
-                self.assertFalse(result)
-        os.remove(temp_output_path)
-        os.remove(diags_file)
-
+            self.assertEqual(result, '')
 
 
 if __name__ == "__main__":

diff --git a/tests/test_data/sv_classifier/output.hyb.vcf.gz b/tests/test_data/sv_classifier/output.hyb.vcf.gz
diff --git a/tests/test_data/sv_classifier/output.ls.vcf.gz b/tests/test_data/sv_classifier/output.ls.vcf.gz
diff --git a/tests/test_data/sv_classifier/output.nb.vcf.gz b/tests/test_data/sv_classifier/output.nb.vcf.gz