diff --git a/gcp_variant_transforms/beam_io/vcf_parser.py b/gcp_variant_transforms/beam_io/vcf_parser.py index 615a6eca7..213fcbe4f 100644 --- 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 index 4e7904278..c080d61a2 100644 --- 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: