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googlegenomics · Sep 18, 2018 · 11bf049 · 11bf049
1 parent 89d9266
commit 11bf049
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Showing 2 changed files with 13 additions and 20 deletions.
diff --git a/gcp_variant_transforms/beam_io/vcf_parser.py b/gcp_variant_transforms/beam_io/vcf_parser.py
@@ -565,7 +565,7 @@ def _get_variant(self, data_line):
     try:
       variant_proto = self._vcf_reader.from_string(data_line)
       return self._convert_to_variant(variant_proto)
-    except (ValueError) as e:
+    except ValueError as e:
       logging.warning('VCF variant_proto read failed in %s for line %s: %s',
                       self._file_name, data_line, str(e))
       return MalformedVcfRecord(self._file_name, data_line, str(e))

diff --git a/gcp_variant_transforms/beam_io/vcfio.py b/gcp_variant_transforms/beam_io/vcfio.py
@@ -212,30 +212,23 @@ def read_records(self,
                    range_tracker  # type: range_trackers.OffsetRangeTracker
                   ):
     # type: (...) -> Iterable[MalformedVcfRecord]
+    vcf_parser_class = None
     if self._vcf_parser_type == VcfParserType.PYVCF:
-      record_iterator = vcf_parser.PyVcfParser(
-          file_name,
-          range_tracker,
-          self._pattern,
-          self._compression_type,
-          self._allow_malformed_records,
-          self._representative_header_lines,
-          buffer_size=self._buffer_size,
-          skip_header_lines=0)
+      vcf_parser_class = vcf_parser.PyVcfParser
     elif self._vcf_parser_type == VcfParserType.NUCLEUS:
-      record_iterator = vcf_parser.NucleusParser(
-          file_name,
-          range_tracker,
-          self._pattern,
-          self._compression_type,
-          self._allow_malformed_records,
-          self._representative_header_lines,
-          buffer_size=self._buffer_size,
-          skip_header_lines=0)
+      vcf_parser_class = vcf_parser.NucleusParser
     else:
       raise ValueError(
           'Unrecognized _vcf_parser_type: %s.' % str(self._vcf_parser_type))
-
+    record_iterator = vcf_parser_class(
+        file_name,
+        range_tracker,
+        self._pattern,
+        self._compression_type,
+        self._allow_malformed_records,
+        self._representative_header_lines,
+        buffer_size=self._buffer_size,
+        skip_header_lines=0)
 
     # Convert iterator to generator to abstract behavior
     for record in record_iterator: