7ed8c6bbcfb2dc0da9b1011ba21d12791239de79,deepvariant/postprocess_variants.py,,main,#Any#,932

Before Change

    record = tf_utils.get_one_example_from_examples_path(
        ",".join(paths), proto=deepvariant_pb2.CallVariantsOutput)
    if record is None:
      raise ValueError("Cannot find any records in {}".format(",".join(paths)))

    sample_name = _extract_single_sample_name(record)
    header = dv_vcf_constants.deepvariant_header(
        contigs=contigs, sample_names=[sample_name])
    use_csi = _decide_to_use_csi(contigs)
    with tempfile.NamedTemporaryFile() as temp:
      start_time = time.time()
      postprocess_variants_lib.process_single_sites_tfrecords(
          contigs, paths, temp.name)
      logging.info("CVO sorting took %s minutes",
                   (time.time() - start_time) / 60)

      logging.info("Transforming call_variants_output to variants.")
      start_time = time.time()
      independent_variants = _transform_call_variants_output_to_variants(
          input_sorted_tfrecord_path=temp.name,
          qual_filter=FLAGS.qual_filter,
          multi_allelic_qual_filter=FLAGS.multi_allelic_qual_filter,

After Change

    record = tf_utils.get_one_example_from_examples_path(
        ",".join(paths), proto=deepvariant_pb2.CallVariantsOutput)
    if record is None:
      logging.info("call_variants_output is empty. Writing out empty VCF.")
      sample_name = dv_constants.DEFAULT_SAMPLE_NAME
      variant_generator = iter([])
    else:
      sample_name = _extract_single_sample_name(record)
      temp = tempfile.NamedTemporaryFile()

Instances