Correctly write meta lines with dictionary value

vcf/parser.py

@@ -158,7 +158,7 @@ def read_meta_hash(self, meta_string):
         # Removing initial hash marks and final equal sign
         key = items[0][2:-1]
         hashItems = items[1].split(',')
-        val = dict(item.split("=") for item in hashItems)
+        val = OrderedDict(item.split("=") for item in hashItems)
         return key, val
 
     def read_meta(self, meta_string):
@@ -549,14 +549,15 @@ def __init__(self, stream, template, lineterminator="\r\n"):
 
         two = '##{key}=<ID={0},Description="{1}">\n'
         four = '##{key}=<ID={0},Number={num},Type={2},Description="{3}">\n'
-        contig_format = '##contig=<ID={ID},length={length},assembly={assembly}>\n'
         _num = self._fix_field_count
         for (key, vals) in template.metadata.iteritems():
             if key in SINGULAR_METADATA:
                 vals = [vals]
             for val in vals:
-                if key == "contig":
-                    stream.write(contig_format.format(**val))
+                if isinstance(val, dict):
+                    values = ','.join('{0}={1}'.format(key, value)
+                                      for key, value in val.items())
+                    stream.write('##{0}=<{1}>\n'.format(key, values))
                 else:
                     stream.write('##{0}={1}\n'.format(key, val))
         for line in template.infos.itervalues():

vcf/test/test_vcf.py

@@ -221,7 +221,7 @@ def testWrite(self):
         out_str = out.getvalue()
         for line in out_str.split("\n"):
             if line.startswith("##contig"):
-                assert "<ID=" in line, "Found dictionary in contig line: {0}".format(line)
+                assert line.startswith('##contig=<'), "Found dictionary in contig line: {0}".format(line)
         print (out_str)
         reader2 = vcf.Reader(out)
 
@@ -257,6 +257,27 @@ def testWrite(self):
             self.assertEquals(l.samples, r.samples)
 
 
+class TestWriterDictionaryMeta(unittest.TestCase):
+
+    def testWrite(self):
+
+        reader = vcf.Reader(fh('example-4.1-bnd.vcf'))
+        out = StringIO()
+        writer = vcf.Writer(out, reader)
+
+        records = list(reader)
+
+        for record in records:
+            writer.write_record(record)
+        out.seek(0)
+        out_str = out.getvalue()
+        for line in out_str.split("\n"):
+            if line.startswith("##PEDIGREE"):
+                self.assertEquals(line, '##PEDIGREE=<Derived="Tumor",Original="Germline">')
+            if line.startswith("##SAMPLE"):
+                assert line.startswith('##SAMPLE=<'), "Found dictionary in meta line: {0}".format(line)
+
+
 class TestRecord(unittest.TestCase):
 
     def test_num_calls(self):
@@ -789,6 +810,7 @@ def test_trim(self):
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestBcfToolsOutput))
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestGatkOutputWriter))
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestBcfToolsOutputWriter))
+suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestWriterDictionaryMeta))
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestTabix))
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestOpenMethods))
 suite.addTests(unittest.TestLoader().loadTestsFromTestCase(TestFilter))